| Name | Mark | System | From | To | Successor | Notes |
| Addison Railroad | | RUT | 1867 | 1951 | N/A | - |
| Addison and Northern Pennsylvania Railway | | B&O | 1882 | 1887 | Addison and Pennsylvania Railway | - |
| Addison and Pennsylvania Railway | | B&O | 1887 | 1898 | Addison and Susquehanna Railroad | - |
| Addison and Susquehanna Railroad | | B&O | 1898 | 1954 | Buffalo and Susquehanna Railroad | - |
| Adirondack Company | | D&H | 1863 | 1882 | Adirondack Railway | - |
| Adirondack Railway | | D&H | 1882 | 1902 | Delaware and Hudson Company | - |
| Adirondack Railway | ADIR | | 1976 | 1981 | | - |
| Adirondac Estate and Railroad Company | | D&H | 1860 | 1863 | Adirondack Company | - |
| Adirondack and St. Lawrence Railroad | | | 1906 | 1925 | N/A | - |
| Albany and Hudson Railway and Power Company | | | 1899 | 1903 | Albany and Hudson Railroad | Electrified in 1900 |
| Albany Northern Railroad | | D&H | 1851 | 1856 | Albany, Vermont and Canada Railroad | - |
| Albany and Schenectady Railroad | | NYC | 1847 | 1853 | New York Central Railroad | - |
| Albany and Susquehanna Railroad | | D&H | 1851 | 1945 | Delaware and Hudson Railroad | - |
| Albany and Vermont Railroad | | D&H | 1859 | | | - |
| Albany, Vermont and Canada Railroad | | D&H | 1856 | 1859 | Albany and Vermont Railroad | - |
| Albany and West Stockbridge Railroad | | NYC | 1836 | 1870 | Boston and Albany Railroad | - |
| Allegany Central Railroad | | PS&N | 1881 | 1883 | Lackawanna and Pittsburgh Railroad | - |
| Amsterdam, Chuctanunda and Northern Railroad | | NYC | 1879 | | | - |
| Atlantic Avenue Railroad | | LIRR | 1872 | 1899 | Nassau Electric Railroad | Main line operated by Long Island Rail Road under a 99-year lease from 1877 |
| Atlantic and Great Western Railroad | | ERIE | 1871 | 1880 | New York, Pennsylvania and Ohio Railroad | - |
| Atlantic and Great Western Railroad | | ERIE | 1859 | 1865 | Atlantic and Great Western Railway | - |
| Atlantic and Great Western Railway | | ERIE | 1865 | 1871 | Atlantic and Great Western Railroad | - |
| Attica and Allegheny Valley Railroad | | | 1852 | 1856 | Attica and Arcade Railroad | - |
| Attica and Buffalo Railroad | | NYC | 1836 | 1850 | Buffalo and Rochester Railroad | - |
| Attica and Arcade Railroad | | | 1870 | 1880 | Tonawanda Valley Railroad | - |
| Attica and Freedom Railroad | | | 1891 | 1894 | Buffalo, Attica and Arcade Railroad | - |
| Attica and Hornellsville Railroad | | ERIE | 1845 | 1851 | Buffalo and New York City Railroad | - |
| Auburn and Ithaca Railway | | LV | 1889 | 1890 | Geneva and Van Ettenville Railway | - |
| Auburn and Rochester Railroad | | NYC | 1836 | 1850 | Rochester and Syracuse Railroad | - |
| Auburn and Syracuse Railroad | | NYC | 1834 | 1850 | Rochester and Syracuse Railroad | - |
| Avon, Geneseo and Mount Morris Railroad | | ERIE | 1860 | 1940 | N/A | - |
| Baltimore and Ohio Railroad | B&O, BO | B&O | 1932 | 1987 | Chesapeake and Ohio Railway | - |
| Bath and Hammondsport Railroad | BH | | 1872 | 1993 | Champagne Railroad | - |
| Battenkill Railroad | | D&H | 1902 | 1903 | Greenwich and Johnsonville Railway | - |
| Bennington and Rutland Railroad | | RUT | 1865 | 1870 | Harlem Extension Railroad | - |
| Bennington and Rutland Railway | | RUT | 1877 | 1901 | Rutland Railroad | - |
| Black River and Morristown Railroad | | NYC | 1870 | 1883 | Utica and Black River Railroad | - |
| Black River and St. Lawrence Railway | | NYC | 1868 | 1883 | Carthage and Adirondack Railway | - |
| Black River and Utica Railroad | | NYC | 1853 | 1860 | Utica and Black River Railroad | - |
| Blossburg and Corning Railroad | | NYC | 1854 | 1873 | Corning, Cowanesque and Antrim Railway | - |
| Bombay and Moira Railroad | | | 1898 | 1898 | N/A | - |
| Boston and Albany Railroad | B&A, BA | NYC | 1870 | 1961 | New York Central Railroad | - |
| Boston, Hartford and Erie Railroad | | NH | 1864 | 1874 | New York and New England Railroad | - |
| Boston, Hartford and Erie Extension Railroad | | NH | 1863 | 1864 | Boston, Hartford and Erie Railroad | - |
| Boston, Hartford and Erie Ferry Extension Railroad | | NH | 1864 | 1864 | Boston, Hartford and Erie Railroad | - |
| Boston, Hoosac Tunnel and Western Railway | | B&M | 1877 | 1892 | Fitchburg Railroad | - |
| Boston and Maine Corporation | BM | B&M | 1964 | | | Still exists as a lessor of Pan Am Railways operating subsidiary Springfield Terminal Railway |
| Boston and Maine Railroad | B&M, BM | B&M | 1900 | 1964 | Boston and Maine Corporation | - |
| Bradford, Eldred and Cuba Railroad | | | 1881 | 1893 | N/A | - |
| Bradford, Richburg and Cuba Railroad | | | 1881 | 1893 | N/A | - |
| Brighton and Bensonhurst Railroad | | | 1892 | | N/A | Never operated |
| Brooklyn, Bath and Coney Island Railroad | BB&CI | BRT/BMT | 1862 | 1885 | Brooklyn, Bath and West End Railroad | - |
| Brooklyn, Bath and West End Railroad | | BRT/BMT | 1885 | 1898 | Atlantic Avenue Railroad | Electrified in 1893 |
| Brooklyn and Brighton Beach Railroad | | BRT/BMT | 1887 | 1899 | Sea View Railroad | - |
| Brooklyn Central and Jamaica Railroad | | LIRR | 1860 | 1865 | Brooklyn and Jamaica Railway | - |
| Brooklyn Eastern District Terminal | BEDT | | 1906 | 1983 | New York Cross Harbor Railroad Terminal Corporation | - |
| Brooklyn, Flatbush and Coney Island Railway | BF&CI | BRT/BMT | 1877 | 1887 | Brooklyn and Brighton Beach Railroad | - |
| Brooklyn and Jamaica Railroad | | LIRR | 1832 | 1860 | Brooklyn Central and Jamaica Railroad | - |
| Brooklyn and Jamaica Railway | | LIRR | 1866 | 1872 | Atlantic Avenue Railroad | - |
| Brooklyn and Montauk Railroad | | LI | 1879 | 1889 | Long Island Rail Road | - |
| Brooklyn and Rockaway Beach Railroad | | BRT/BMT | 1863 | 1906 | Canarsie Railroad | - |
| Buffalo and Allegheny Valley Railroad | | PRR | 1853 | 1865 | Buffalo and Washington Railway | - |
| Buffalo, Attica and Arcade Railroad | | | 1894 | 1917 | Arcade and Attica Railroad | - |
| Buffalo and Black Rock Railroad | | | 1833 | 1851 | | - |
| Buffalo, Bradford and Pittsburgh Railroad | | ERIE | 1859 | 1941 | Erie Railroad | - |
| Buffalo Branch of the Erie Railway | | ERIE | 1861 | 1862 | Erie Railway | - |
| Buffalo, Chautauqua Lake and Pittsburgh Railway | | PRR | 1879 | 1880 | Pittsburgh, Titusville and Buffalo Railway | - |
| Buffalo, Cleveland and Chicago Railway | | NKP | 1881 | 1881 | New York, Chicago and St. Louis Railway | - |
| Buffalo and Cohocton Valley Railway | | ERIE | 1850 | 1852 | Buffalo, Corning and New York Railroad | - |
| Buffalo, Corning and New York Railroad | | ERIE | 1852 | 1857 | Buffalo, New York and Erie Railroad | - |
| Buffalo, Corry and Pittsburgh Railroad | | PRR | 1867 | 1872 | Dunkirk, Chautauqua Lake and Pittsburgh Railroad | - |
| Buffalo Creek Railroad | BCK | ERIE/ LV | 1869 | 1983 | Consolidated Rail Corporation | - |
| Buffalo Creek Transfer Railroad | | | 1881 | 1914 | N/A | - |
| Buffalo and Erie Railroad | | NYC | 1867 | 1869 | Lake Shore and Michigan Southern Railway | - |
| Buffalo Erie Basin Railroad | | NYC | 1876 | 1913 | New York Central and Hudson River Railroad | - |
| Buffalo Extension of the Atlantic and Great Western Railway | | ERIE | 1864 | 1865 | Atlantic and Great Western Railway | - |
| Buffalo and Geneva Railroad | | LV | 1889 | 1890 | Lehigh Valley Railway | - |
| Buffalo and Jamestown Railroad | | ERIE | 1872 | 1877 | Buffalo and South Western Railroad | - |
| Buffalo and Lockport Railroad | | NYC | 1852 | 1853 | New York Central Railroad | - |
| Buffalo and New York City Railroad | | ERIE | 1851 | 1861 | Buffalo Branch of the Erie Railway, Buffalo, New York and Erie Railroad | - |
| Buffalo, New York and Erie Railroad | | ERIE | 1857 | 1896 | Erie Railroad | - |
| Buffalo, New York and Philadelphia Railroad | | PRR | 1883 | 1887 | Western New York and Pennsylvania Railway of New York | - |
| Buffalo, New York and Philadelphia Railway | | PRR | 1871 | 1883 | Buffalo, New York and Philadelphia Railroad | - |
| Buffalo and Niagara Falls Railroad | | NYC | 1834 | 1869 | New York Central Railroad | - |
| Buffalo and Oil Creek Cross Cut Railroad | | PRR | 1865 | 1867 | Buffalo, Corry and Pittsburgh Railroad | - |
| Buffalo and Pittsburgh Railroad | | ERIE | 1852 | 1859 | Buffalo, Bradford and Pittsburgh Railroad | - |
| Buffalo, Pittsburgh and Western Railroad | | PRR | 1881 | 1883 | Buffalo, New York and Philadelphia Railroad | - |
| Buffalo, Pittsburgh and Western Railway | | PRR | 1880 | 1881 | Buffalo, Pittsburgh and Western Railroad | - |
| Buffalo and Rochester Railroad | | NYC | 1850 | 1853 | New York Central Railroad | - |
| Buffalo, Rochester and Pittsburgh Railroad | | B&O | 1885 | 1887 | Buffalo, Rochester and Pittsburgh Railway | - |
| Buffalo, Rochester and Pittsburgh Railroad | | B&O | 1881 | 1881 | Rochester and Pittsburgh Railroad | - |
| Buffalo, Rochester and Pittsburgh Railway | BR&P | B&O | 1887 | | | Still exists as a nonoperating subsidiary of CSX Transportation, leased to the Buffalo and Pittsburgh Railroad |
| Buffalo and South Western Railroad | | ERIE | 1877 | 1895 | Erie Railroad | - |
| Buffalo and State Line Railroad | | NYC | 1848 | 1867 | Buffalo and Erie Railroad | - |
| Buffalo and Susquehanna Railroad | | B&O | 1954 | 1954 | Baltimore and Ohio Railroad | - |
| Buffalo and Susquehanna Railroad | B&S | B&O | 1910 | 1932 | Baltimore and Ohio Railroad | - |
| Buffalo and Susquehanna Railroad | | B&O | 1896 | 1907 | Buffalo and Susquehanna Railway | - |
| Buffalo and Susquehanna Railway | | | 1902 | 1915 | Wellsville and Buffalo Railroad | - |
| Buffalo, Thousand Islands & Portland Railroad | | NYC | 1850 | 1907 | Rome, Watertown and Ogdensburg Railroad | - |
| Buffalo and Washington Railroad | | PRR | 1865 | 1865 | Buffalo and Washington Railway | - |
| Buffalo and Washington Railway | | PRR | 1865 | 1871 | Buffalo, New York and Philadelphia Railway | - |
| Bush Terminal Railroad | | | 1903 | 1971 | New York Cross Harbor Railroad | - |
| Cairo Railroad | | | 1884 | 1918 | N/A | - |
| Campbell Hall Connecting Railroad | | LNE | 1889 | 1961 | N/A | - |
| Canada Southern Railway | CASO | NYC | 1883 | 1904 | Michigan Central Railroad | - |
| Canajoharie and Catskill Railroad | | | 1830 | 1842 | Catskill Mountain Railroad | - |
| Canal Railroad | | LV | 1878 | 1905 | Lehigh Valley Railway | - |
| Canandaigua and Corning Railroad | | PRR | 1845 | 1852 | Canandaigua and Elmira Railroad | - |
| Canandaigua and Elmira Railroad | | PRR | 1852 | 1857 | Elmira, Canandaigua and Niagara Falls Railroad | - |
| Canandaigua Lake Railroad | | PRR | 1887 | 1888 | Elmira and Lake Ontario Railroad | - |
| Canandaigua and Niagara Falls Railroad | | NYC | 1851 | 1857 | Niagara Bridge and Canandaigua Railroad | - |
| Canarsie Railroad | | BRT/BMT | 1906 | 1912 | New York Consolidated Railroad | Electrified in 1906 |
| Canastota Northern Railroad | | LV | 1886 | 1905 | Elmira, Cortland and Northern Railroad | - |
| Carthage and Adirondack Railway | | NYC | 1883 | 1913 | New York Central and Hudson River Railroad | - |
| Carthage and Copenhagen Railroad | | | 1906 | 1917 | Deer River Railroad | - |
| Carthage, Watertown and Sackets Harbor Railroad | | NYC | 1869 | 1913 | New York Central and Hudson River Railroad | - |
| Castleton and West Stockbridge Railroad | | NYC | 1834 | 1836 | Albany and West Stockbridge Railroad | - |
| Catskill Mountain Railroad | | | 1917 | 1918 | N/A | - |
| Catskill Mountain Railroad | | | 1880 | 1885 | Catskill Mountain Railway | - |
| Catskill Mountain Railway | | | 1885 | 1916 | Catskill Mountain Railroad | - |
| Catskill and Tannersville Railway | | | 1892 | 1916 | Catskill Mountain Railroad | - |
| Cayuga Railway | | LV | 1874 | 1877 | Cayuga Southern Railroad | - |
| Cayuga Lake Railroad | | LV | 1867 | 1874 | Cayuga Railway | - |
| Cayuga Southern Railroad | | LV | 1877 | 1879 | Geneva, Ithaca and Sayre Railroad | - |
| Cayuga and Susquehanna Railroad | | DL&W | 1843 | 1946 | Delaware, Lackawanna and Western Railroad | - |
| Cazenovia and Canastota Railroad | | LV | 1868 | 1873 | Cazenovia and Canastota Railway | - |
| Cazenovia and Canastota Railway | | LV | 1873 | 1873 | Cazenovia, Canastota and De Ruyter Railroad | - |
| Cazenovia, Canastota and De Ruyter Railroad | | LV | 1873 | 1876 | Cazenovia, Canastota and De Ruyter Railway | - |
| Cazenovia, Canastota and De Ruyter Railway | | LV | 1876 | 1884 | Elmira, Cortland and Northern Railroad | - |
| Cazenovia and De Ruyter Railroad | | LV | 1872 | 1873 | Cazenovia, Canastota and De Ruyter Railroad | - |
| Central Railroad Extension Company | | LI | 1873 | 1882 | Long Island Rail Road | - |
| Central Railroad of Long Island | | LI | 1871 | 1879 | Long Island Rail Road | - |
| Central New England Railway | CNE | NH | 1899 | 1927 | New York, New Haven and Hartford Railroad | - |
| Central New England and Western Railroad | | NH | 1889 | 1892 | Philadelphia, Reading and New England Railroad | - |
| Central New York and Northern Railroad | | PS&N | 1899 | 1899 | Central New York and Western Railroad | - |
| Central New York Southern Railroad | | | 1914 | 1923 | N/A | - |
| Central New York and Western Railroad | | PS&N | 1892 | 1899 | Pittsburg, Shawmut and Northern Railroad | - |
| Central Valley Railroad | | | 1870 | 1875 | N/A | - |
| Central Vermont Railroad | | CN | 1873 | 1899 | Central Vermont Railway | - |
| Central Vermont Railway | CV | CN | 1898 | 1962 | N/A | - |
| Champagne Railroad | CGNE | | 1993 | 1996 | Livonia, Avon and Lakeville Railroad | - |
| Champlain and St. Lawrence Railroad | | CN | 1851 | 1960 | Canadian National Railway | - |
| Chateaugay Railroad | | D&H | 1879 | 1903 | Chateaugay and Lake Placid Railway | - |
| Chateaugay Railway | | D&H | 1887 | 1903 | Chateaugay and Lake Placid Railway | - |
| Chateaugay and Lake Placid Railway | | D&H | 1903 | 1957 | Delaware and Hudson Railroad | - |
| Chatham and Lebanon Valley Railroad | | RUT | 1899 | 1901 | Rutland Railroad | - |
| Chautauqua Lake Railway | | | 1886 | 1894 | Jamestown and Lake Erie Railway | - |
| Chemung Railroad | | PRR | 1845 | 1886 | Elmira and Lake Ontario Railroad | - |
| Cherry Valley and Mohawk River Railroad | | D&H | 1864 | 1869 | Cherry Valley, Sharon and Albany Railroad | - |
| Cherry Valley, Sharon and Albany Railroad | | D&H | 1869 | 1908 | Delaware and Hudson Company | - |
| Cherry Valley and Sprakers Railroad | | D&H | 1860 | 1864 | Cherry Valley and Mohawk River Railroad | - |
| Chesapeake and Ohio Railway | C&O, CO | C&O | 1947 | 1987 | CSX Transportation | - |
| Clayton and Theresa Railroad | | NYC | 1871 | 1886 | Utica and Black River Railroad | - |
| Clove Branch Railroad | | | 1868 | 1898 | N/A | - |
| Conesus Lake Railroad | | ERIE | 1882 | 1932 | Erie Railroad | - |
| Coney Island and East River Railway | | | 1876 | 1877 | Brooklyn, Flatbush and Coney Island Railway | - |
| Conhocton Valley Railroad | | | 2001 | 2001 | B&H Rail Corporation | - |
| Connecting Terminal Railroad | | PRR | 1881 | 1931 | Western New York and Pennsylvania Railway | - |
| Consolidated Rail Corporation | CR | | 1976 | 1999 | CSX Transportation, Norfolk Southern Railway | - |
| Cooperstown and Charlotte Valley Railroad | | D&H | 1888 | 1957 | Delaware and Hudson Railroad | - |
| Cooperstown and Charlotte Valley Railway | CACV | | 1971 | 1989 | N/A | - |
| Cooperstown and Susquehanna Valley Railroad | | D&H | 1865 | 1957 | Delaware and Hudson Railroad | - |
| Corning and Blossburg Railroad | | NYC | 1851 | 1852 | Blossburg and Corning Railroad | - |
| Corning, Cowanesque and Antrim Railway | | NYC | 1873 | 1892 | Fall Brook Railway | - |
| Cornwall Bridge Company | | NYC | 1897 | 1917 | New York Central Railroad | - |
| Cranberry Lake Railroad | | | 1902 | 1914 | N/A | - |
| Danbury Terminal Railroad | DTRR | | 1993 | 1996 | Housatonic Railroad | - |
| Dansville and Mount Morris Railroad | D&MM, DMM | | 1891 | | | Still exists as a nonoperating subsidiary of the Rochester and Southern Railroad |
| Deer River Railroad | | | 1917 | 1918 | N/A | - |
| Degnon Terminal Railroad | | LIRR | 1913 | 1928 | Long Island Rail Road | - |
| Delaware and Eastern Railroad | | | 1904 | 1911 | Delaware and Northern Railroad | - |
| Delaware and Eastern Railway | | | 1907 | 1911 | Delaware and Northern Railroad | - |
| Delaware and Hudson Company | | D&H | 1899 | 1930 | Delaware and Hudson Railroad | - |
| Delaware and Hudson Railroad | D&H | D&H | 1930 | 1968 | Delaware and Hudson Railway | - |
| Delaware and Hudson Canal Company | | D&H | 1867 | 1899 | Delaware and Hudson Company | - |
| Delaware, Lackawanna and Western Railroad | DL&W, DLW | DL&W | 1870 | 1960 | Erie–Lackawanna Railroad | - |
| Delaware and Northern Railroad | D&N | | 1911 | 1928 | Delaware and Northern Railway | - |
| Delaware and Northern Railway | D&N | | 1928 | 1942 | N/A | - |
| Delaware and Otsego Railroad | | NYC | 1887 | 1901 | Ulster and Delaware Railroad | - |
| Depew and Tonawanda Railroad | | LV | 1895 | 1903 | Lehigh Valley Railway | - |
| Dexter and Northern Railroad | | | 1908 | 1956 | N/A | - |
| Direct Railway between Syracuse and Rochester | | NYC | 1848 | 1850 | Rochester and Syracuse Railroad | - |
| Dolgeville and Salisbury Railway | | NYC | 1907 | 1917 | New York Central Railroad | - |
| Dunkirk, Allegheny Valley and Pittsburgh Railroad | | NYC | 1873 | 1914 | New York Central Railroad | - |
| Dunkirk, Chautauqua Lake and Pittsburgh Railroad | | PRR | 1879 | 1879 | Buffalo, Chautauqua Lake and Pittsburgh Railway | - |
| Dunkirk and State Line Railroad | | NYC | 1850 | 1851 | Buffalo and State Line Railroad | - |
| Dunkirk, Warren and Pittsburgh Railroad | | NYC | 1867 | 1870 | Dunkirk, Warren and Pittsburgh Railway | - |
| Dunkirk, Warren and Pittsburgh Railway | | NYC | 1870 | 1873 | Dunkirk, Allegheny Valley and Pittsburgh Railroad | - |
| Dutchess and Columbia Railroad | | NH | 1866 | 1872 | New York, Boston and Northern Railway | - |
| Dutchess County Railroad | | NH | 1890 | 1907 | Central New England Railway | - |
| East River Terminal Railroad | | | 1907 | 1916 | Brooklyn Eastern District Terminal | - |
| Ellenville and Kingston Railroad | | NH | 1901 | 1957 | N/A | - |
| Elmira, Canandaigua and Niagara Falls Railroad | | PRR | 1857 | 1858 | Elmira, Jefferson and Canandaigua Railroad | - |
| Elmira, Cortland and Northern Railroad | | LV | 1884 | 1905 | Lehigh Valley Railway | - |
| Elmira, Jefferson and Canandaigua Railroad | | PRR | 1859 | 1886 | Elmira and Lake Ontario Railroad | - |
| Elmira and Lake Ontario Railroad | | PRR | 1886 | 1956 | Northern Central Railway | - |
| Elmira State Line Railroad | | ERIE | 1872 | 1942 | N/A | - |
| Elmira and Williamsport Railroad | | PRR | 1860 | 1969 | Penndel Company | - |
| Erie Railroad | ERIE | ERIE | 1895 | 1960 | Erie–Lackawanna Railroad | - |
| Erie Railway | | ERIE | 1861 | 1878 | New York, Lake Erie and Western Railroad | - |
| Erie and Black Rock Railroad | | ERIE | 1882 | 1932 | Erie Railroad | - |
| Erie and Central New York Railroad | | DL&W | 1902 | 1945 | Delaware, Lackawanna and Western Railroad | - |
| Erie and Central New York Railway | | DL&W | 1863 | 1902 | Erie and Central New York Railroad | - |
| Erie and Genesee Valley Railroad | | ERIE | 1868 | 1891 | Dansville and Mount Morris Railroad | - |
| Erie International Railway | | ERIE | 1872 | 1895 | Erie Railroad | - |
| Erie and Jersey Railroad | | ERIE | 1905 | 1915 | Erie Railroad | - |
| Erie–Lackawanna Railroad | EL | | 1960 | 1968 | Erie Lackawanna Railway | - |
| Erie Lackawanna Railway | EL | | 1968 | 1976 | Consolidated Rail Corporation | - |
| Erie and New York City Railroad | | ERIE | 1851 | 1860 | Atlantic and Great Western Railroad | - |
| Erie Terminals Railroad | | ERIE | 1907 | 1915 | Erie Railroad | - |
| Fall Brook Railway | | NYC | 1892 | 1909 | Geneva, Corning and Southern Railroad | - |
| Far Rockaway Branch Railroad | | LI | 1868 | 1872 | South Side Railroad of Long Island | - |
| Fitchburg Railroad | | B&M | 1887 | 1919 | Boston and Maine Railroad | - |
| Flatbush and Coney Island Park and Concourse Railroad | | | 1876 | 1877 | Brooklyn, Flatbush and Coney Island Railway | - |
| Flushing Railroad | | LI | 1852 | 1859 | New York and Flushing Railroad | - |
| Flushing and North Side Railroad | | LI | 1868 | 1881 | Long Island City and Flushing Railroad | - |
| Flushing and Woodside Railroad | | LI | 1864 | 1871 | Flushing and North Side Railroad | - |
| Fonda, Johnstown and Gloversville Railroad | FJG | | 1867 | 1984 | N/A | - |
| Friendship Railroad | | PS&N | 1880 | 1881 | Allegany Central Railroad | - |
| Fulton Chain Railroad | | NYC | 1896 | 1902 | Fulton Chain Railway | - |
| Fulton Chain Railway | | NYC | 1902 | 1937 | New York Central Railroad | - |
| Fulton and Oswego Railroad | | NYC | 1885 | 1886 | Syracuse, Phoenix and Oswego Railway | - |
| Garnerville Railroad | | ERIE | 1875 | | N/A | - |
| Genesee Falls Railway | | NYC | 1886 | | | - |
| Genesee River Railroad | | ERIE | 1905 | 1915 | Erie Railroad | - |
| Genesee Valley Canal Railroad | | PRR | 1880 | 1912 | Pennsylvania and Rochester Railroad | - |
| Genesee Valley Terminal Railroad | | PRR | 1882 | 1912 | Pennsylvania and Rochester Railroad | - |
| Genesee and Wyoming Railroad | GNW, GNWR | | 1899 | | | Still exists as a nonoperating subsidiary of the Rochester and Southern Railroad |
| Genesee and Wyoming Valley Railway | | | 1891 | 1899 | Genesee and Wyoming Railroad | - |
| Geneseo Valley Railroad | | ERIE | 1857 | 1860 | Avon, Geneseo and Mount Morris Railroad | - |
| Geneva, Corning and Southern Railroad | | NYC | 1909 | 1914 | New York Central Railroad | - |
| Geneva, Corning and Southern Railway | | NYC | 1875 | 1909 | Geneva, Corning and Southern Railroad | - |
| Geneva and Hornellsville Railway | | PRR | 1875 | 1876 | Geneva, Hornellsville and Pine Creek Railway | - |
| Geneva, Hornellsville and Pine Creek Railway | | PRR | 1876 | 1879 | Lake Ontario Southern Railway | - |
| Geneva and Ithaca Railroad | | LV | 1870 | 1874 | Geneva, Ithaca and Athens Railroad | - |
| Geneva, Ithaca and Athens Railroad | | LV | 1874 | 1876 | Geneva, Ithaca and Sayre Railroad | - |
| Geneva, Ithaca and Sayre Railroad | | LV | 1876 | 1889 | Geneva and Sayre Railroad | - |
| Geneva and Lyons Railroad | | NYC | 1877 | 1890 | New York Central and Hudson River Railroad | - |
| Geneva and Sayre Railroad | | LV | 1889 | 1890 | Geneva and Van Ettenville Railway | - |
| Geneva and Southwestern Railway | | PRR | 1871 | 1875 | Geneva and Hornellsville Railway | - |
| Geneva Southwestern and Hornellsville Railway | | PRR | 1872 | 1875 | Geneva and Hornellsville Railway | - |
| Geneva and Van Ettenville Railway | | LV | 1889 | 1890 | Lehigh Valley Railway | - |
| Glen Cove Branch Rail Road | | LI | 1865 | | Long Island Rail Road | - |
| Glendale and East River Railroad | | LI | 1874 | 1928 | Long Island Rail Road | - |
| Glenfield and Western Railroad | | | 1901 | | N/A | - |
| Glens Falls Railroad | | D&H | 1867 | 1906 | Rensselaer and Saratoga Railroad | - |
| Gloversville and Broadalbin Railroad | | | 1895 | 1931 | Fonda, Johnstown and Gloversville Railroad | - |
| Gloversville and Northville Railroad | | | 1872 | 1881 | Fonda, Johnstown and Gloversville Railroad | - |
| Goshen and Deckertown Railway | | ERIE | 1868 | 1954 | Erie Railroad | - |
| Gouverneur and Oswegatchie Railroad | | NYC | 1892 | 1913 | New York Central and Hudson River Railroad | - |
| Grand Trunk Railway | GT | CN | 1864 | 1923 | Canadian National Railway | - |
| Grasse River Railroad | GR | | 1915 | 1959 | N/A | - |
| Great Neck and Port Washington Railroad | | LI | 1896 | 1902 | Long Island Rail Road | - |
| Great Valley and Bradford Railroad | | B&O | 1881 | 1881 | Rochester and Pittsburgh Railroad | - |
| Great Western Railway | | CN | 1855 | 1882 | Grand Trunk Railway | - |
| Greigsville and Pearl Creek Railroad | | | 1897 | 1899 | N/A | - |
| Greene Railroad | | DL&W | 1869 | 1946 | Delaware, Lackawanna and Western Railroad | - |
| Greenwich and Johnsonville Railroad | | D&H | 1874 | 1879 | Greenwich and Johnsonville Railway | - |
| Greenwich and Johnsonville Railway | G&J, GJ | D&H | 1879 | 1982 | Batten Kill Railroad | - |
| Greenwood and Coney Island Railroad | | | 1872 | 1874 | Prospect Park and Coney Island Railroad | - |
| Hackensack and New York Extension Railroad | | ERIE | 1869 | 1873 | New Jersey and New York Railway | - |
| Halite and Northern Railroad | | | 1910 | 1933 | N/A | - |
| Hancock and East Branch Railroad | | | 1906 | 1907 | Delaware and Eastern Railway | - |
| Hancock and Pennsylvania Railroad | | NH | 1889 | 1889 | Ontario, Carbondale and Scranton Railway | - |
| Harlem Extension Railroad | | RUT | 1870 | 1873 | New York, Boston and Montreal Railway | - |
| Harlem Extension Railroad South Coal Transportation Company | | RUT | 1877 | 1880 | N/A | Leased the New York, Boston and Montreal Railway |
| Harlem River and Port Chester Railroad | | NH | 1866 | 1927 | New York, New Haven and Hartford Railroad | - |
| Hartford and Connecticut Western Railroad | | NH | 1882 | 1947 | New York, New Haven and Hartford Railroad | - |
| Hayts Corners, Ovid and Willard Railroad | | LV | 1882 | 1959 | N/A | - |
| Hempstead and Rockaway Railroad | | LIRR | 1869 | 1871 | New York and Hempstead Railroad | - |
| Herkimer, Newport and Poland Railway | | NYC | 1891 | 1892 | Mohawk and Malone Railway | - |
| Herkimer, Newport and Poland Extension Railway | | NYC | 1891 | 1892 | Mohawk and Malone Railway | - |
| Herkimer, Newport and Poland Narrow Gauge Railway | | NYC | 1880 | 1891 | Herkimer, Newport and Poland Railway | - |
| Hicksville and Cold Spring Branch Railroad | | LI | 1853 | 1870 | Long Island Rail Road | - |
| Hobart Branch Railroad | | NYC | 1884 | 1901 | Ulster and Delaware Railroad | - |
| Hoosac Tunnel and Saratoga Railway | | B&M | 1881 | 1886 | Troy, Saratoga and Northern Railroad | - |
| Hudson and Berkshire Railroad | | NYC | 1832 | 1854 | Hudson and Boston Railroad | - |
| Hudson and Boston Railroad | | NYC | 1855 | 1870 | Boston and Albany Railroad | - |
| Hudson Connecting Railroad | | NH | 1887 | 1889 | Central New England and Western Railroad | - |
| Hudson Light and Power and Railroad Company | | | 1899 | 1899 | Albany and Hudson Railway and Power Company | - |
| Hudson River Railroad | | NYC | 1846 | 1869 | New York Central and Hudson River Railroad | - |
| Hudson River Bridge Company at Albany | | NYC | 1856 | 1976 | Consolidated Rail Corporation | - |
| Hudson River Connecting Railroad | | NYC | 1913 | 1964 | New York Central Railroad | - |
| Hudson River West Shore Railroad | | NYC | 1867 | 1868 | West Shore Hudson River Railroad | - |
| Hunter's Point and South Side Railroad | | LI | 1870 | 1872 | South Side Railroad of Long Island | - |
| International Bridge Company | | CN | 1857 | 1956 | Canadian National Railway | - |
| Island Railroad | | | 1883 | | | - |
| Ithaca and Athens Railroad | | LV | 1870 | 1874 | Geneva, Ithaca and Athens Railroad | - |
| Ithaca, Auburn and Western Railroad | | LV | 1876 | 1890 | Auburn and Ithaca Railway | - |
| Ithaca and Cortland Railroad | | LV | 1869 | 1871 | Utica, Ithaca and Elmira Railroad | - |
| Ithaca and Owego Railroad | | DL&W | 1828 | 1843 | Cayuga and Susquehanna Railroad | - |
| Ithaca and Tonawanda Railroad | | LV | 1865 | 1870 | Ithaca and Athens Railroad | - |
| Jamaica and South Shore Railroad | | LI | 1903 | 1912 | Long Island Rail Road | - |
| Jamestown and Chautauqua Railway | | | 1898 | 1913 | Jamestown, Westfield and Northwestern Railroad | - |
| Jamestown, Chautauqua and Lake Erie Railway | | | 1900 | 1913 | Jamestown, Westfield and Northwestern Railroad | - |
| Jamestown and Lake Erie Railway | | | 1894 | 1898 | Jamestown and Chautauqua Railway | - |
| Jamestown, Westfield and Northwestern Railroad | | | 1913 | 1950 | N/A | Electric from 1914 to 1947 |
| Jay Street Connecting Railroad | | | 1909 | | | - |
| Jay Street Extension Railroad | | | 1916 | 1916 | Jay Street Connecting Railroad | - |
| Jersey City and Albany Railroad | | NYC | 1873 | 1877 | Jersey City and Albany Railway | - |
| Jersey City and Albany Railway | | NYC | 1878 | 1881 | North River Railroad | - |
| Junction Railroad | | NYC | 1870 | 1879 | New York Central and Hudson River Railroad | - |
| Kaaterskill Railroad | | NYC | 1882 | 1901 | Ulster and Delaware Railroad | - |
| Kanona and Prattsburg Railroad | | | 1886 | 1893 | Kanona and Prattsburg Railway | - |
| Kanona and Prattsburg Railway | | | 1897 | 1917 | Prattsburg Railway | - |
| Keeseville, Ausable Chasm and Lake Champlain Railroad | | | 1889 | 1924 | N/A | Electric from 1905 to 1911 |
| Kinderhook and Hudson Railway | | | 1889 | 1899 | Hudson Light and Power and Railroad Company | - |
| Kings County Central Railroad | | | 1876 | 1878 | N/A | - |
| Lackawanna and Pittsburgh Railroad | | PS&N | 1882 | 1889 | Lackawanna and Southwestern Railroad | - |
| Lackawanna and Southwestern Railroad | | PS&N | 1889 | 1892 | Central New York and Western Railroad | - |
| Lackawanna and Susquehanna Railroad | | D&H | 1867 | | | - |
| Lake Champlain and Moriah Railroad | | | 1867 | 1968 | N/A | - |
| Lake Ontario Railroad | | NYC | 1874 | 1875 | Rome, Watertown and Ogdensburg Railroad | - |
| Lake Ontario and Hudson River Railroad | | D&H | 1857 | 1860 | Adirondac Estate and Railroad Company | - |
| Lake Ontario Shore Railroad | | NYC | 1868 | 1874 | Lake Ontario Railroad | - |
| Lake Ontario Southern Railway | | PRR | 1879 | 1882 | Sodus Bay and Southern Railroad | - |
| Lake Shore and Michigan Southern Railway | | NYC | 1869 | 1914 | New York Central Railroad | - |
| Lebanon Springs Railroad | | RUT | 1893 | 1899 | Chatham and Lebanon Valley Railroad | - |
| Lebanon Springs Railroad | | RUT | 1852 | 1870 | Harlem Extension Railroad | - |
| Lehigh – Buffalo Terminal Railway | | LV | 1915 | | | - |
| Lehigh and Hudson River Railway | L&HR, LHR | L&HR | 1882 | 1976 | Consolidated Rail Corporation | - |
| Lehigh and Lake Erie Railroad | | LV | 1896 | 1907 | Lehigh Valley Railway | - |
| Lehigh and New England Railroad | LNE | LNE | 1895 | 1961 | N/A | - |
| Lehigh and New York Railroad | | LV | 1895 | 1949 | Lehigh Valley Railroad | - |
| Lehigh Valley Railroad | LV | LV | 1888 | 1976 | Consolidated Rail Corporation | - |
| Lehigh Valley Railway | | LV | 1882 | 1949 | Lehigh Valley Railroad | - |
| Lewiston Railroad | | NYC | 1836 | 1855 | New York Central Railroad | - |
| Lincoln Park and Charlotte Railroad | | B&O | 1888 | 1899 | Buffalo, Rochester and Pittsburgh Railway | - |
| Little Falls and Dolgeville Railroad | | NYC | 1891 | 1913 | New York Central and Hudson River Railroad | - |
| Lockport and Buffalo Railway | | ERIE | 1871 | 1895 | Erie Railroad | - |
| Lockport and Niagara Falls Railroad | | NYC | 1834 | 1850 | Rochester, Lockport and Niagara Falls Railroad | - |
| Long Island Rail Road | LI | LI | 1834 | 1997 | New York and Atlantic Railway | Still exists as a passenger railroad |
| Long Island Railroad North Shore Branch | | LI | 1892 | 1921 | Long Island Rail Road | - |
| Long Island City and Flushing Railroad | | LI | 1881 | 1889 | Long Island Rail Road | - |
| Long Island City and Manhattan Beach Railroad | | LI | 1883 | 1885 | New York, Brooklyn and Manhattan Beach Railway | - |
| Mahopac Falls Railroad | | NYC | 1884 | 1913 | New York and Putnam Railroad | - |
| Malone and St. Lawrence Railway | | NYC | 1891 | 1895 | St. Lawrence and Adirondack Railway | - |
| Marcellus Electric Railroad | | | 1887 | 1905 | Marcellus and Otisco Lake Railway | - |
| Marcellus and Otisco Company | | | 1919 | 1959 | N/A | - |
| Marcellus and Otisco Lake Railway | | | 1905 | 1920 | Marcellus and Otisco Company | - |
| Marion Railway | | PRR | 1917 | 1931 | Elmira and Lake Ontario Railroad | - |
| Massena Springs and Fort Covington Railroad | | CN | 1884 | 1888 | United States and Canada Railroad | - |
| Mayville Extension Railroad | | | 1881 | 1887 | Chautauqua Lake Railway | - |
| Mechanicville and Fort Edward Railroad | | B&M | 1880 | | | - |
| Michigan Central Railroad | MC | NYC | 1904 | 1930 | New York Central Railroad | - |
| Middleburgh and Schoharie Railroad | | | 1867 | 1936 | N/A | - |
| Middlesex Valley Railroad | | LV | 1892 | 1903 | Lehigh Valley Railway | - |
| Middletown and Crawford Railroad | | ERIE | 1868 | 1932 | Erie Railroad | - |
| Middletown and New Jersey Railway | MNJ | | 1947 | 2009 | Middletown and New Jersey Railroad | - |
| Middletown and Unionville Railroad | M&U, MU | | 1913 | 1947 | Middletown and New Jersey Railway | - |
| Middletown, Unionville and Water Gap Railroad | | ERIE | 1866 | 1913 | Middletown and Unionville Railroad | - |
| Midland Railroad of New Jersey | | ERIE | 1880 | 1881 | New York, Susquehanna and Western Railroad | - |
| Mohawk and Adirondack Railroad | | NYC | 1891 | 1891 | Herkimer, Newport and Poland Extension Railway, St. Lawrence and Adirondack Railroad | - |
| Mohawk and Hudson Railroad | | NYC | 1826 | 1847 | Albany and Schenectady Railroad | - |
| Mohawk and Malone Railway | | NYC | 1892 | 1913 | New York Central and Hudson River Railroad | - |
| Mohawk Valley Railroad | | NYC | 1851 | 1853 | New York Central Railroad | - |
| Mohawk Valley and Northern Railway | | NYC | 1890 | 1891 | Herkimer, Newport and Poland Narrow Gauge Railway | - |
| Montauk Extension Railroad | | LI | 1893 | 1902 | Long Island Rail Road | - |
| Montclair Railway | | ERIE | 1867 | 1875 | Montclair and Greenwood Lake Railway | - |
| Montclair and Greenwood Lake Railway | | ERIE | 1875 | 1878 | New York and Greenwood Lake Railway | - |
| Montgomery and Erie Railway | | ERIE | 1866 | 1954 | Erie Railroad | - |
| Monticello and Port Jervis Railway | | NH | 1869 | 1875 | Port Jervis and Monticello Railroad | - |
| Montreal and Champlain Railroad | | CN | 1857 | 1864 | Grand Trunk Railway | - |
| Montreal and Plattsburgh Railroad | | D&H | 1868 | 1873 | New York and Canada Railroad | - |
| Mount McGregor Railroad | | | 1889 | 1897 | Saratoga and Mount McGregor Railway | - |
| Nanuet and New City Railroad | | ERIE | 1871 | | New Jersey and New York Railroad | - |
| Napierville Junction Railway | NJ | D&H | | | | Still exists as a nonoperating subsidiary of the Canadian Pacific Railway |
| New England Railroad | | NH | 1895 | 1908 | New York, New Haven and Hartford Railroad | - |
| New Jersey Midland Railway | | ERIE | 1874 | 1880 | Midland Railroad of New Jersey | - |
| New Jersey and New York Railroad | | ERIE | 1880 | 1967 | Erie–Lackawanna Railroad | - |
| New Jersey and New York Railway | | ERIE | 1873 | 1880 | New Jersey and New York Railroad | - |
| New Jersey and New York Extension Railroad | | ERIE | 1886 | 1936 | New Jersey and New York Railroad | - |
| New York and Albany Railroad | | NYC | 1832 | 1846 | New York and Harlem Railroad | - |
| New York and Atlantic Railway | | | 1880 | 1887 | West Brooklyn Railroad | - |
| New York, Auburn and Lansing Railroad | | | 1900 | 1914 | Central New York Southern Railroad | - |
| New York Bay Extension Railroad | | LI | 1892 | 1902 | Long Island Rail Road | - |
| New York, Bay Ridge and Jamaica Railroad | | LI | 1875 | 1885 | New York, Brooklyn and Manhattan Beach Railway | - |
| New York and Boston Railroad | | NYC | 1869 | 1872 | New York, Boston and Northern Railway | - |
| New York, Boston and Montreal Railway | | NH, NYC, RUT | 1873 | 1876 | Bennington and Rutland Railway, New York, Rutland and Montreal Railroad, New York, Westchester and Putnam Railway, Newburgh, Dutchess and Connecticut Railroad | - |
| New York, Boston and Northern Railway | | NH, NYC | 1872 | 1873 | New York, Boston and Montreal Railway | - |
| New York and Brighton Beach Railway | | | 1878 | 1884 | Sea Beach and Brighton Railroad | - |
| New York, Brooklyn and Manhattan Beach Railway | | LI | 1885 | 1925 | Long Island Rail Road | - |
| New York and Canada Railroad | | D&H | 1872 | 1908 | Delaware and Hudson Company | - |
| New York Central Railroad | NYC | NYC | 1914 | 1968 | Penn Central Transportation Company | - |
| New York Central Railroad | | NYC | 1853 | 1869 | New York Central and Hudson River Railroad | - |
| New York Central and Hudson River Railroad | | NYC | 1869 | 1914 | New York Central Railroad | - |
| New York Central Niagara River Railroad | | NYC | 1877 | 1913 | New York Central and Hudson River Railroad | - |
| New York, Chicago and St. Louis Railroad | NKP | NKP | 1887 | 1964 | Norfolk and Western Railway | - |
| New York, Chicago and St. Louis Railway | | NKP | 1881 | 1887 | New York, Chicago and St. Louis Railroad | - |
| New York City and Northern Railroad | | NYC | 1878 | 1887 | New York and Northern Railway | - |
| New York and Coney Island Railroad | | | 1879 | | South Brooklyn Railway | Electrified in 1899 |
| New York Connecting Railroad | NYCN | NH/ PRR | 1892 | 1976 | Consolidated Rail Corporation | - |
| New York Cross Harbor Railroad Terminal Corporation | NYCH | | 1983 | 2006 | New York New Jersey Rail, LLC | - |
| New York Dock Railway | NYD | | 1910 | 1983 | New York Cross Harbor Railroad Terminal Corporation | - |
| New York and Eastern Railway | NYER | | 2003 | 2004 | N/A | Never operated |
| New York and Erie Railroad | | ERIE | 1832 | 1861 | Erie Railway | - |
| New York and Flushing Railroad | | LI | 1859 | 1891 | Long Island Rail Road | - |
| New York and Greenwood Lake Railway | | ERIE | 1878 | 1943 | Erie Railroad | - |
| New York and Harlem Railroad | | NYC | 1831 | | | Still exists as a lessor of the Metro-North Commuter Railroad |
| New York and Hempstead Railroad | | LIRR | 1871 | 1875 | Southern Hempstead Branch Railroad | - |
| New York and Hempstead Plains Railroad | | LIRR | 1870 | 1871 | New York and Hempstead Railroad | - |
| New York, Housatonic and Northern Railroad | | | 1863 | 1881 | Westchester Railway | - |
| New York and Jamaica Railroad | | LI | 1859 | 1860 | Long Island Rail Road | - |
| New York, Kingston and Syracuse Railroad | | NYC | 1872 | 1875 | Ulster and Delaware Railroad | - |
| New York, Lackawanna and Western Railway | | DL&W | 1880 | 1945 | Delaware, Lackawanna and Western Railroad | - |
| New York, Lake Erie and Western Railroad | | ERIE | 1878 | 1895 | Erie Railroad | - |
| New York and Long Beach Railroad | | LI | 1880 | 1907 | Long Island Rail Road | - |
| New York and Mahopac Railroad | | NYC | 1871 | 1880 | New York and Harlem Railroad | - |
| New York and Manhattan Beach Railway | NY&MB | LI | 1876 | 1885 | New York, Brooklyn and Manhattan Beach Railway | - |
| New York and Massachusetts Railway | | NH | 1887 | 1893 | Poughkeepsie and Eastern Railway | - |
| New York and New England Railroad | | NH | 1873 | 1895 | New England Railroad | - |
| New York and New Haven Railroad | | NH | 1846 | 1872 | New York, New Haven and Hartford Railroad | - |
| New York, New Haven and Hartford Railroad | NH | NH | 1872 | 1969 | Penn Central Transportation Company | - |
| New York and Northern Railway | | NYC | 1887 | 1893 | New York and Putnam Railroad | - |
| New York, Ontario and Western Railway | O&W, OW | NH | 1880 | 1957 | N/A | - |
| New York and Oswego Midland Railroad | | NH | 1866 | 1879 | Ithaca, Auburn and Western Railroad, New York, Ontario and Western Railway | - |
| New York and Ottawa Railroad | | NYC | 1897 | 1904 | New York and Ottawa Railway | - |
| New York and Ottawa Railway | | NYC | 1905 | 1913 | New York Central and Hudson River Railroad | - |
| New York, Pennsylvania and Ohio Railroad | | ERIE | 1880 | 1896 | Nypano Railroad | - |
| New York and Pennsylvania Railroad | | | 1896 | 1902 | New York and Pennsylvania Railway | - |
| New York and Pennsylvania Railway | | | 1904 | 1935 | N/A | - |
| New York and Putnam Railroad | | NYC | 1894 | 1913 | New York Central and Hudson River Railroad | - |
| New York and Rockaway Railroad | | LI | 1870 | 1903 | Jamaica and South Shore Railroad | - |
| New York and Rockaway Beach Railway | | LI | 1887 | 1921 | Long Island Rail Road | - |
| New York, Rutland and Montreal Railroad | | RUT | 1883 | 1893 | Lebanon Springs Railroad | - |
| New York and Sea Beach Railway | NY&SB | BRT/BMT | 1876 | 1896 | Sea Beach Railway | - |
| New York, Susquehanna and Western Railroad | | ERIE | 1881 | 1958 | N/A | - |
| New York, West Shore and Buffalo Railway | | NYC | 1880 | 1885 | West Shore Railroad | - |
| New York, West Shore and Chicago Railroad | | NYC | 1870 | 1879 | New York, West Shore and Buffalo Railway | - |
| New York, Westchester and Boston Railway | | | 1912 | 1937 | N/A | Partly owned by the New York, New Haven and Hartford Railroad |
| New York, Westchester and Putnam Railway | | NYC | 1877 | 1878 | New York City and Northern Railroad | - |
| New York, Woodhaven and Rockaway Railroad | | LI | 1877 | 1887 | New York and Rockaway Beach Railway | - |
| Newark and Marion Railway | | PRR | 1900 | 1917 | Marion Railway | - |
| Newburgh, Dutchess and Connecticut Railroad | | NH | 1877 | 1907 | Central New England Railway | - |
| Newburgh and New York Railway | | ERIE | 1865 | 1895 | New York, Lake Erie and Western Railroad | - |
| Newton Falls and Northern Railroad | | | 1908 | 1919 | N/A | - |
| Newtown and Flushing Railroad | | LIRR | 1871 | 1876 | N/A | - |
| Niagara Bridge and Canandaigua Railroad | | NYC | 1858 | 1890 | New York Central and Hudson River Railroad | - |
| Niagara Falls Branch Railroad | | NYC | 1875 | 1913 | New York Central and Hudson River Railroad | - |
| Niagara Falls International Bridge Company | | CN | 1846 | | | - |
| Niagara Junction Railway | NJ, NIAJ | ERIE/ LV/ NYC | 1892 | 1976 | Consolidated Rail Corporation | Electrified in 1913 |
| Niagara River Bridge Company | | NYC | 1881 | 2002 | N/A | Still exists as an abandoned subsidiary of CNCP Niagara–Windsor Partnership, a nonoperating joint subsidiary of the Canadian National Railway and Canadian Pacific Railway |
| Nickel Plate Connecting Railroad | | NKP | 1917 | | | - |
| Norfolk and Western Railway | N&W, NW | | 1964 | 1998 | Norfolk Southern Railway | - |
| North River Railroad | | NYC | 1881 | 1881 | New York, West Shore and Buffalo Railway | - |
| North River Railway | | NYC | 1880 | 1881 | North River Railroad | - |
| North Shore Railroad | | LI | 1863 | 1884 | Long Island City and Flushing Railroad | - |
| Northern Railroad | | RUT | 1845 | 1865 | Ogdensburg and Lake Champlain Railroad | - |
| Northern Railroad of New Jersey | | ERIE | 1858 | 1943 | Erie Railroad | - |
| Northern Adirondack Railroad | | NYC | 1883 | 1895 | Northern New York Railroad | - |
| Northern Adirondack Extension Railroad | | NYC | 1886 | 1890 | Northern Adirondack Railroad | - |
| Northern Central Railway | | PRR | 1956 | 1976 | Consolidated Rail Corporation | - |
| Northern Central Railway | | PRR | 1863 | 1911 | Pennsylvania Railroad | - |
| Northern Extension of the Rochester, Nunda and Pennsylvania Railroad | | PRR | 1872 | 1872 | Rochester, Nunda and Pennsylvania Railroad | - |
| Northern New York Railroad | | NYC | 1895 | 1897 | New York and Ottawa Railroad | - |
| Norwood and Montreal Railroad | | NYC | 1884 | 1889 | Rome, Watertown and Ogdensburg Railroad | - |
| Norwood and St. Lawrence Railroad | NSL | | 1901 | 1974 | Ogdensburg and Norwood Railway | - |
| Nyack and Northern Railroad | | ERIE | 1868 | 1892 | Nyack and Southern Railroad | - |
| Nyack and Southern Railroad | | ERIE | 1899 | 1944 | Erie Railroad | - |
| Nypano Railroad | | ERIE | 1896 | 1941 | Erie Railroad | - |
| Ogdensburg and Lake Champlain Railroad | | RUT | 1864 | 1898 | Ogdensburg and Lake Champlain Railway | - |
| Ogdensburg and Lake Champlain Railway | | RUT | 1898 | 1899 | Rutland Railroad | - |
| Ogdensburg and Morristown Railroad | | NYC | 1871 | 1886 | Utica and Black River Railroad | - |
| Ogdensburg and Norwood Railway | ONRY | | 1965 | 1977 | St. Lawrence Railroad | - |
| Olean Railroad | | PS&N | 1880 | 1881 | Allegany Central Railroad | - |
| Olean, Bradford and Warren Railroad | | PRR | 1877 | 1916 | Western New York and Pennsylvania Railway | - |
| Olean and Salamanca Railroad | | PRR | 1882 | 1883 | Buffalo, New York and Philadelphia Railroad | - |
| Ontario, Carbondale and Scranton Railway | | NH | 1889 | 1957 | N/A | - |
| Ontario Eastern Railroad | ONER | | 1981 | 1987 | N/A | - |
| Ontario Southern Railroad | | PRR | 1875 | 1879 | Lake Ontario Southern Railway | - |
| Orange County Railroad | | L&HR | 1888 | 1907 | Lehigh and Hudson River Railway | - |
| Oswego Railroad Bridge Company | | NYC | 1872 | 1885 | Rome, Watertown and Ogdensburg Railroad | - |
| Oswego and Rome Railroad | | NYC | 1863 | 1913 | New York Central and Hudson River Railroad | - |
| Oswego and Syracuse Railroad | | DL&W | 1839 | 1945 | Delaware, Lackawanna and Western Railroad | - |
| Otis Railway | | | 1899 | 1916 | Catskill Mountain Railroad | - |
| Otis Elevating Railway | | | 1885 | 1899 | Otis Railway | - |
| Owasco River Railway | OR | LV/ NYC | 1881 | 1976 | N/A | - |
| Oyster Bay Extension Railroad | | LI | 1886 | 1913 | Long Island Rail Road | |
| Pan Am Railways | PAR | NY, New England | 1981 | 2022 | CSX Transportation | - |
| Pecksport Connecting Railway | | NH | 1886 | 1957 | N/A | - |
| Peekskill Valley Railroad | | | 1873 | | N/A | long gauge |
| Penn Central Transportation Company | PC | | 1968 | 1976 | Consolidated Rail Corporation | - |
| Penn Yan and New York Railway | | NYC | 1877 | 1885 | Syracuse, Geneva and Corning Railway | |
| Penndel Company | | PRR | 1955 | 1976 | Consolidated Rail Corporation | - |
| Pennsylvania Railroad | PRR | PRR | 1900 | 1968 | Penn Central Transportation Company | - |
| Pennsylvania, New York and Long Island Railroad | | PRR | 1902 | 1907 | Pennsylvania Tunnel and Terminal Railroad | - |
| Pennsylvania and New York Canal and Railroad Company | | LV | 1867 | 1888 | Lehigh Valley Railroad | - |
| Pennsylvania, Poughkeepsie and Boston Railroad | | LNE | 1887 | 1895 | Lehigh and New England Railroad | - |
| Pennsylvania and Rochester Railroad | | PRR | 1912 | 1916 | Western New York and Pennsylvania Railway | - |
| Pennsylvania Tunnel and Terminal Railroad | | PRR | 1907 | 1976 | Consolidated Rail Corporation | - |
| Pere Marquette Railroad | | C&O | 1904 | 1917 | Pere Marquette Railway | - |
| Pere Marquette Railway | PM | C&O | 1917 | 1947 | Chesapeake and Ohio Railway | - |
| Perry Railroad | | B&O | 1882 | 1899 | Buffalo, Rochester and Pittsburgh Railway | - |
| Philadelphia, Reading and New England Railroad | | NH | 1892 | 1899 | Central New England Railway | - |
| Pine Plains and Albany Railroad | | RUT | 1872 | 1872 | Harlem Extension Railroad | - |
| Pittsburgh and New York Railroad | | B&O | 1881 | 1881 | Rochester and Pittsburgh Railroad | - |
| Pittsburg, Shawmut and Northern Railroad | | PS&N | 1899 | 1947 | N/A | - |
| Pittsburgh, Titusville and Buffalo Railway | | PRR | 1880 | 1881 | Buffalo, Pittsburgh and Western Railroad | - |
| Plattsburgh and Dannemora Railroad | | D&H | 1878 | | | - |
| Plattsburgh and Montreal Railroad | | D&H | 1850 | 1868 | Montreal and Plattsburgh Railroad | - |
| Pochuck Railroad | | LNE | 1897 | 1944 | N/A | - |
| Port Chester Terminal Railroad | | | 1901 | | | - |
| Port Dickinson and Chenango River Railroad | | DL&W | 1881 | | N/A | - |
| Port Jervis and Monticello Railroad | | NH | 1875 | 1886 | Port Jervis, Monticello and New York Railroad | - |
| Port Jervis, Monticello and New York Railroad | | NH | 1886 | 1902 | Port Jervis, Monticello and Summitville Railroad | - |
| Port Jervis, Monticello and Summitville Railroad | | NH | 1902 | 1957 | N/A | - |
| Potsdam and Watertown Railroad | | NYC | 1852 | 1860 | Watertown and Rome Railroad | - |
| Poughkeepsie Bridge Company | | NH | 1871 | 1892 | Poughkeepsie Bridge and Railroad Company | - |
| Poughkeepsie Bridge Railroad | | NH | 1888 | 1907 | Central New England Railway | - |
| Poughkeepsie Bridge and Railroad Company | | NH | 1892 | 1892 | Philadelphia, Reading and New England Railroad | - |
| Poughkeepsie and Connecticut Railroad | | NH | 1888 | 1889 | Central New England and Western Railroad | - |
| Poughkeepsie and Eastern Railroad | | NH | 1866 | 1875 | Poughkeepsie, Hartford and Boston Railroad | - |
| Poughkeepsie and Eastern Railway | | NH | 1893 | 1907 | Central New England Railway | - |
| Poughkeepsie, Hartford and Boston Railroad | | NH | 1875 | 1887 | Hartford and Connecticut Western Railroad, New York and Massachusetts Railway | - |
| Prattsburg Railway | | | 1917 | 1962 | N/A | - |
| Prospect Park and Coney Island Railroad | PP&CI | | 1874 | | | Electrified in 1899 |
| Prospect Park and South Brooklyn Railroad | PP&SB | | 1888 | | | Electrified in 1899 |
| Putnam and Dutchess Railroad | | | 1871 | 1872 | New York, Boston and Northern Railway | - |
| Raquette Lake Railway | | NYC | 1899 | 1933 | N/A | - |
| Raymondville and Waddington Railroad | | | 1907 | 1908 | Norwood and St. Lawrence Railroad | - |
| Rensselaer and Saratoga Railroad | | D&H | 1832 | 1945 | Delaware and Hudson Railroad | - |
| Rhinebeck and Connecticut Railroad | | NH | 1870 | 1882 | Hartford and Connecticut Western Railroad | - |
| R.J. Corman Railroad/Allentown Lines | RJCN | | 1996 | 2002 | N/A | - |
| Rochester and Charlotte Railroad | | B&O | 1881 | 1881 | Rochester and Pittsburgh Railroad | - |
| Rochester and Genesee Valley Railroad | | ERIE | 1851 | 1976 | Consolidated Rail Corporation | - |
| Rochester and Honeoye Valley Railroad | | LV | 1888 | 1895 | Rochester Southern Railroad | - |
| Rochester, Hornellsville and Lackawanna Railroad | | PS&N | 1886 | 1889 | Lackawanna and Southwestern Railroad | - |
| Rochester, Hornellsville and Pine Creek Railroad | | PRR | 1872 | 1876 | Geneva, Hornellsville and Pine Creek Railway | - |
| Rochester and Lake Beach Railroad | | NYC | 1888 | 1888 | Rome, Watertown and Ogdensburg Terminal Railroad | - |
| Rochester and Lake Ontario Railroad | | NYC | 1852 | 1855 | New York Central Railroad | - |
| Rochester, Lockport and Niagara Falls Railroad | | NYC | 1850 | 1853 | New York Central Railroad | - |
| Rochester, New York and Pennsylvania Railroad | | PRR, PS&N | 1881 | 1916 | Allegany Central Railroad, Western New York and Pennsylvania Railway | - |
| Rochester, Nunda and Pennsylvania Railroad | | PRR, PS&N | 1870 | 1877 | Rochester, Nunda and Pittsburgh Railroad | - |
| Rochester, Nunda and Pennsylvania Extension Railroad | | PS&N | 1872 | 1872 | Rochester, Nunda and Pennsylvania Railroad | - |
| Rochester, Nunda and Pittsburgh Railroad | | PRR | 1877 | 1881 | Rochester, New York and Pennsylvania Railroad | - |
| Rochester and Ontario Belt Railway | | NYC | 1882 | 1887 | Rochester and Lake Beach Railroad | - |
| Rochester and Pine Creek Railroad | | B&O | 1870 | 1877 | Silver Lake Railroad | - |
| Rochester and Pittsburgh Railroad | | B&O | 1881 | 1885 | Buffalo, Rochester and Pittsburgh Railroad | - |
| Rochester Southern Railroad | | LV | 1895 | 1903 | Lehigh Valley Railway | - |
| Rochester and Southern Railroad | | LV | 1895 | 1895 | Rochester Southern Railroad | - |
| Rochester and State Line Railroad | | B&O | 1869 | 1881 | Rochester and Pittsburgh Railroad | - |
| Rochester and Syracuse Railroad | | NYC | 1850 | 1853 | New York Central Railroad | - |
| Rockaway Railway | | LI | 1871 | 1872 | South Side Railroad of Long Island | - |
| Rockland Central Railroad | | NYC | 1870 | 1873 | Jersey City and Albany Railroad | - |
| Rockland Central Extension Railroad | | NYC | 1872 | 1872 | Rockland Central Railroad | - |
| Rome and Clinton Railroad | | NH | 1869 | 1944 | New York, Ontario and Western Railway | - |
| Rome, Watertown and Ogdensburg Railroad | | NYC | 1861 | 1913 | New York Central and Hudson River Railroad | - |
| Rome, Watertown and Ogdensburg Terminal Railroad | | NYC | 1886 | 1890 | Rome, Watertown and Ogdensburg Railroad | - |
| Rondout and Oswego Railroad | | NYC | 1866 | 1872 | New York, Kingston and Syracuse Railroad | - |
| Rutland Railroad | RUT | RUT | 1899 | 1950 | Rutland Railway | - |
| Rutland Railway | RUT | RUT | 1950 | 1961 | New York Central Railroad | - |
| Rutland–Canadian Railroad | | RUT | 1898 | 1901 | Rutland Railroad | - |
| Rutland and Washington Railroad | | D&H | 1850 | 1865 | Troy, Salem and Rutland Railroad | - |
| Sackets Harbor and Ellisburg Railroad | | | 1851 | 1858 | Sackett's Harbor, Rome and New York Railroad | - |
| Sackett's Harbor, Rome and New York Railroad | | | 1860 | 1862 | N/A | - |
| Sackets Harbor and Saratoga Railroad | | D&H | 1852 | 1857 | Lake Ontario and Hudson River Railroad | - |
| St. Lawrence Railroad | SLAW | | 1977 | 1990 | St. Lawrence and Raquette River Railroad | - |
| St. Lawrence and Adirondack Railroad | | NYC | 1891 | 1892 | Mohawk and Malone Railway | - |
| St. Lawrence and Adirondack Railway | | NYC | 1895 | | | Still exists as a nonoperating subsidiary of CSX Transportation |
| St. Lawrence and Hudson Railway | STLH | CP | 1996 | 2001 | Canadian Pacific Railway | - |
| St. Lawrence and Raquette River Railroad | SLRR | | 1990 | 1998 | New York and Ogdensburg Railway | - |
| Salamanca, Bradford and Allegheny River Railroad | | PRR | 1880 | 1881 | Buffalo, Pittsburgh and Western Railroad | - |
| Saranac and Lake Placid Railroad | | D&H | 1890 | 1903 | Chateaugay and Lake Placid Railway | - |
| Saratoga and Fort Edward Railroad | | D&H | 1832 | | Saratoga and Washington Railroad | - |
| Saratoga and Hudson River Railroad | | NYC | 1864 | 1867 | New York Central Railroad | - |
| Saratoga Lake Railway | | B&M | 1880 | 1886 | Troy, Saratoga and Northern Railroad | - |
| Saratoga and Mount McGregor Railway | | | 1897 | 1898 | Saratoga Northern Railway | - |
| Saratoga and North Creek Railway | | | 2011 | 2018 | | - |
| Saratoga, Mount McGregor and Lake George Railroad | | | 1882 | 1888 | Mount McGregor Railroad | - |
| Saratoga Northern Railway | | | 1899 | 1901 | Hudson Valley Railway | - |
| Saratoga and St. Lawrence Railroad | | | 1885 | 1897 | Bombay and Moira Railroad | - |
| Saratoga and Schenectady Railroad | | D&H | 1831 | | | - |
| Saratoga and Schuylerville Railroad | | | 1945 | 1956 | N/A | - |
| Saratoga and Washington Railroad | | D&H | 1834 | 1855 | Saratoga and Whitehall Railroad | - |
| Saratoga and Whitehall Railroad | | D&H | 1855 | 1868 | Rensselaer and Saratoga Railroad | - |
| Schenectady and Duanesburgh Railroad | | D&H | 1873 | 1903 | Delaware and Hudson Company | - |
| Schenectady and Margaretville Railroad | | | 1906 | 1907 | Delaware and Eastern Railway | - |
| Schenectady and Mechanicville Railroad | | D&H | 1867 | | | - |
| Schenectady and Susquehanna Railroad | | D&H | 1869 | 1873 | Schenectady and Duanesburgh Railroad | - |
| Schenectady and Troy Railroad | | NYC | 1836 | 1853 | New York Central Railroad | - |
| Schoharie Valley Railroad | | D&H | 1865 | 1874 | Schoharie Valley Railway | - |
| Schoharie Valley Railway | | D&H | 1880 | 1941 | N/A | - |
| Schuylerville and Upper Hudson Railroad | | B&M | 1869 | 1877 | Mechanicville and Fort Edward Railroad | - |
| Scottsville and LeRoy Railroad | | | 1836 | | N/A | - |
| Sea Beach Railway | | | 1896 | 1912 | New York Consolidated Railroad | Electrified in 1898 |
| Sea Beach and Brighton Railroad | | | 1886 | 1892 | Brighton and Bensonhurst Railroad | - |
| Seneca County Railway | | LV | 1891 | 1903 | Lehigh Valley Railway | - |
| Sharon and Ceres Terminal Railroad | | | 1904 | 1904 | New York and Pennsylvania Railway | - |
| Shawmut Connecting Railroad | | PS&N | 1900 | 1905 | Pittsburg, Shawmut and Northern Railroad | - |
| Silver Creek and Dunkirk Railway | | NYC | 1890 | 1894 | Lake Shore and Michigan Southern Railway | - |
| Silver Lake Railroad | | B&O | 1877 | 1886 | Silver Lake Railway | - |
| Silver Lake Railroad | | B&O | 1869 | | Rochester and Pine Creek Railroad | - |
| Silver Lake Railway | | B&O | 1886 | 1910 | Buffalo, Rochester and Pittsburgh Railway | - |
| Skaneateles Railroad | | | 1866 | 1941 | Skaneateles Short Line Railroad | - |
| Skaneateles Railroad | | | 1836 | 1841 | Skaneateles and Jordan Railroad | - |
| Skaneateles and Jordan Railroad | | | 1841 | 1851 | N/A | - |
| Skaneateles Short Line Railroad | SSL | | 1940 | 1981 | N/A | - |
| Smithtown and Port Jefferson Railroad | | LI | 1870 | 1892 | Long Island Railroad North Shore Branch | - |
| Sodus Bay and Southern Railroad | | PRR | 1882 | 1886 | Elmira and Lake Ontario Railroad | - |
| Sodus Point and Southern Railroad | | PRR | 1852 | 1875 | Ontario Southern Railroad | - |
| South Brooklyn Railroad and Terminal Company | | | 1887 | 1899 | South Brooklyn Railway | - |
| South Brooklyn Railway | SBK | | 1900 | | | Electric until 1961 |
| South Brooklyn and Flatbush Railroad | | | 1885 | 1887 | South Brooklyn Railroad and Terminal Company | - |
| South Side Railroad of Long Island | | LI | 1860 | 1874 | Southern Railroad of Long Island | - |
| Southern Railroad of Long Island | | LI | 1874 | 1880 | Brooklyn and Montauk Railroad | - |
| Southern Central Railroad | | LV | 1865 | 1895 | Lehigh and New York Railroad | - |
| Southern Hempstead Branch Railroad | | LIRR | 1875 | 1882 | Stewart Railroad | - |
| Southern New York Railroad | | | 1888 | 1970 | N/A | - |
| Southern Westchester Railroad | | | 1871 | 1872 | New York, Housatonic and Northern Railroad | - |
| Southfield Branch Railroad | | | 1868 | 1894 | N/A | - |
| Springville and Sardinia Railroad | | | 1878 | 1886 | N/A | - |
| Spuyten Duyvil and Port Morris Railroad | | NYC | 1867 | 1913 | New York Central and Hudson River Railroad | - |
| Staten Island Railroad | SIRC | B&O | 1971 | 1991 | N/A | - |
| Staten Island Railroad | | B&O | 1851 | 1872 | Staten Island Railway | - |
| Staten Island Railway | | B&O | 1873 | 1944 | Staten Island Rapid Transit Railway | - |
| Staten Island Rapid Transit Railroad | | B&O | 1880 | 1899 | Staten Island Rapid Transit Railway | - |
| Staten Island Rapid Transit Railway | SIR | B&O | 1899 | 1971 | Staten Island Railroad | - |
| Sterling Mountain Railway | | | 1864 | 1955 | N/A | - |
| Stewart Railroad | | LIRR | 1873 | 1892 | Long Island Rail Road | - |
| Stony Clove and Catskill Mountain Railroad | | NYC | 1881 | 1901 | Ulster and Delaware Railroad | - |
| Suffern Railroad | | ERIE | 1907 | 1907 | Erie and Jersey Railroad | - |
| Suspension Bridge and Erie Junction Railroad | | ERIE | 1868 | 1896 | Erie Railroad | - |
| Syracuse and Baldwinsville Railroad | | DL&W | 1886 | 1891 | Syracuse and Baldwinsville Railway | - |
| Syracuse and Baldwinsville Railway | | DL&W | 1891 | | N/A | - |
| Syracuse and Binghamton Railroad | | DL&W | 1851 | 1856 | Syracuse and Southern Railroad | - |
| Syracuse, Binghamton and New York Railroad | | DL&W | 1857 | 1945 | Delaware, Lackawanna and Western Railroad | - |
| Syracuse and Chenango Railroad | | NYC | 1873 | 1877 | Syracuse, Chenango and New York Railroad | - |
| Syracuse and Chenango Valley Railroad | | NYC | 1868 | 1873 | Syracuse and Chenango Railroad | - |
| Syracuse, Chenango and New York Railroad | | NYC | 1877 | 1883 | Syracuse, Ontario and New York Railway | - |
| Syracuse, Geneva and Corning Railway | | NYC | 1875 | 1909 | Geneva, Corning and Southern Railroad | - |
| Syracuse Junction Railroad | | NYC | 1873 | 1879 | New York Central and Hudson River Railroad | - |
| Syracuse Northern Railroad | | NYC | 1868 | 1875 | Syracuse and Northern Railroad | - |
| Syracuse and Northern Railroad | | NYC | 1875 | 1875 | Rome, Watertown and Ogdensburg Railroad | - |
| Syracuse Northwestern Railroad | | NYC | 1874 | 1875 | Syracuse, Phoenix and Oswego Railroad | - |
| Syracuse, Ontario and New York Railway | | NYC | 1883 | 1891 | West Shore Railroad | - |
| Syracuse, Phoenix and Oswego Railroad | | NYC | 1871 | 1885 | Syracuse, Phoenix and Oswego Railway | - |
| Syracuse, Phoenix and Oswego Railway | | NYC | 1885 | 1889 | Rome, Watertown and Ogdensburg Railroad | - |
| Syracuse and Southern Railroad | | DL&W | 1856 | 1857 | Syracuse, Binghamton and New York Railroad | - |
| Syracuse and Utica Railroad | | NYC | 1836 | 1853 | New York Central Railroad | - |
| Syracuse and Utica Direct Railroad | | NYC | 1853 | 1853 | New York Central Railroad | - |
| Terminal Railway of Buffalo | | NYC | 1895 | 1914 | New York Central Railroad | - |
| Ticonderoga Railroad | | D&H | 1889 | 1957 | Delaware and Hudson Railroad | - |
| Tioga Railroad | | ERIE | 1876 | 1885 | New York, Lake Erie and Western Railroad | - |
| Tioga Central Railroad | TIOC | | 1987 | 1992 | Owego and Harford Railway | - |
| Tioga Coal, Iron Mining and Manufacturing Company | | NYC | 1833 | 1851 | Corning and Blossburg Railroad | - |
| Tivoli Hollow Railroad | | NYC | 1893 | 1913 | New York Central and Hudson River Railroad | - |
| Tonawanda Railroad | | NYC | 1832 | 1850 | Buffalo and Rochester Railroad | - |
| Tonawanda Island Railroad | TIRL | | 1983 | 1996 | N/A | - |
| Tonawanda Island Bridge Company | | NYC | 1883 | 1913 | New York Central and Hudson River Railroad | - |
| Tonawanda Valley Railroad | | | 1880 | 1881 | Tonawanda Valley and Cuba Railroad | - |
| Tonawanda Valley and Cuba Railroad | | | 1881 | 1886 | Attica and Freedom Railroad | - |
| Tonawanda Valley Extension Railroad | | | 1880 | 1881 | Tonawanda Valley and Cuba Railroad | - |
| Troy and Bennington Railroad | | B&M | 1851 | 1946 | Boston and Maine Railroad | - |
| Troy and Boston Railroad | | B&M | 1848 | 1887 | Fitchburg Railroad | - |
| Troy and Greenbush Railroad | | NYC | 1845 | 1976 | Consolidated Rail Corporation | - |
| Troy and Rutland Railroad | | D&H | 1849 | 1865 | Troy, Salem and Rutland Railroad | - |
| Troy, Salem and Rutland Railroad | | D&H | 1865 | 1868 | Rensselaer and Saratoga Railroad | - |
| Troy, Saratoga and Northern Railroad | | B&M | 1886 | 1892 | Fitchburg Railroad | - |
| Troy Union Railroad | | B&M/ D&H/ NYC | 1851 | 1964 | N/A | - |
| Tunesassa and Bradford Railroad | | | 1905 | | | - |
| Ulster and Delaware Railroad | | NYC | 1875 | 1932 | New York Central Railroad | - |
| Unadilla Valley Railway | UV | | 1890 | 1960 | N/A | - |
| Union Railroad | | ERIE | 1851 | 1946 | Erie Railroad | - |
| Union Railroad | | DL&W | 1856 | 1858 | Syracuse, Binghamton and New York Railroad | - |
| Union Terminal Railroad of Buffalo | | PRR | 1884 | 1917 | Western New York and Pennsylvania Railway | - |
| Union Village and Johnsonville Railroad | | D&H | 1866 | 1874 | Greenwich and Johnsonville Railroad | - |
| United States and Canada Railroad | | CN | 1883 | 1960 | Canadian National Railway | - |
| Upper Hudson Railroad | | B&M | 1872 | 1872 | Schuylerville and Upper Hudson Railroad | - |
| Utica and Black River Railroad | | NYC | 1860 | 1913 | New York Central and Hudson River Railroad | - |
| Utica, Chenango and Cortland Railroad | | DL&W | 1870 | 1883 | Erie and Central New York Railway | - |
| Utica, Chenango and Susquehanna Valley Railway | | DL&W | 1866 | 1945 | Delaware, Lackawanna and Western Railroad | - |
| Utica City Railroad | | NH | 1862 | 1866 | Utica and Waterville Railroad | - |
| Utica, Clinton and Binghamton Railroad | | NH | 1868 | 1942 | New York, Ontario and Western Railway | - |
| Utica, Horseheads and Elmira Railroad | | LV | 1870 | 1871 | Utica, Ithaca and Elmira Railroad | - |
| Utica, Ithaca and Elmira Railroad | | LV | 1871 | 1878 | Utica, Ithaca and Elmira Railway | - |
| Utica, Ithaca and Elmira Railway | | LV | 1878 | 1884 | Elmira, Cortland and Northern Railroad | - |
| Utica and Schenectady Railroad | | NYC | 1833 | 1853 | New York Central Railroad | - |
| Utica and Unadilla Valley Railroad | | | 1888 | 1895 | Unadilla Valley Railway | - |
| Utica and Waterville Railroad | | NH | 1866 | 1868 | Utica, Clinton and Binghamton Railroad | - |
| Valley Railroad | | DL&W | 1869 | 1945 | Delaware, Lackawanna and Western Railroad | - |
| Vermont and Canada Railroad | | CN | 1845 | 1891 | Central Vermont Railroad | - |
| Vermont Central Railroad | | CN | 1870 | 1873 | Central Vermont Railroad | - |
| Vermont Central Railroad | | CN | 1849 | 1855 | N/A | Leased the Vermont and Canada Railroad |
| Wabash Railroad | | WAB | 1898 | 1915 | Wabash Railway | - |
| Wabash Railroad | WAB | WAB | 1942 | 1964 | Norfolk and Western Railway | - |
| Wabash Railway | | WAB | 1915 | 1942 | Wabash Railroad | - |
| Wallkill Valley Railroad | | NYC | 1877 | 1952 | New York Central Railroad | - |
| Wallkill Valley Railway | | NYC | 1866 | 1877 | Wallkill Valley Railroad | - |
| Warwick Valley Railroad | | L&HR | 1860 | 1882 | Lehigh and Hudson River Railway | - |
| Watertown and Rome Railroad | | NYC | 1832 | 1861 | Rome, Watertown and Ogdensburg Railroad | - |
| Waverly and State Line Railway | | LV | 1867 | 1903 | Lehigh Valley Railway | - |
| Wellsville, Addison and Galeton Railroad | WAG | | 1954 | 1973 | N/A | - |
| Wellsville, Bradford and Eldred Railroad | | | 1881 | 1893 | N/A | - |
| Wellsville and Buffalo Railroad | | | 1915 | 1916 | N/A | - |
| Wellsville, Coudersport and Pine Creek Railroad | | B&O | 1881 | 1954 | Buffalo and Susquehanna Railroad | - |
| West Brooklyn Railroad | | | 1887 | 1889 | N/A | - |
| West Davenport Railroad | | D&H | 1891 | 1891 | Cooperstown and Charlotte Valley Railroad | - |
| West Shore Railroad | | NYC | 1885 | 1952 | New York Central Railroad | - |
| West Shore Hudson River Railroad | | NYC | 1867 | 1877 | New York, West Shore and Chicago Railroad | - |
| West Side and Yonkers Railway | | NYC | 1879 | 1887 | New York City and Northern Railroad | - |
| West Troy and Green Island Railroad | | D&H | 1870 | | | - |
| Westchester Railway | | | 1881 | | N/A | - |
| Western New York Railway | | PRR | 1895 | 1895 | Western New York and Pennsylvania Railway | - |
| Western New York and Pennsylvania Railroad | | PRR | 1887 | 1895 | Western New York and Pennsylvania Railway | - |
| Western New York and Pennsylvania Railway | | PRR | 1895 | 1955 | Penndel Company | - |
| Western New York and Pennsylvania Railway of New York | | PRR | 1887 | 1887 | Western New York and Pennsylvania Railroad | - |
| Western Vermont Railroad | | RUT | 1845 | 1865 | Bennington and Rutland Railroad | - |
| Wharton Valley Railway | | NH | 1888 | 1942 | N/A | - |
| Whitehall and Plattsburgh Railroad | | D&H | 1866 | 1873 | New York and Canada Railroad | - |
| Whitestone and Westchester Railroad | | LI | 1871 | 1887 | Long Island City and Flushing Railroad | - |
| Williamsport and Elmira Railroad | | PRR | 1850 | 1860 | Elmira and Williamsport Railroad | - |
| Williamstown and Redfield Railroad | | | 1865 | | N/A | - |
| Windsor Beach and Ontario Railroad | | NYC | 1887 | 1888 | Rome, Watertown and Ogdensburg Terminal Railroad | - |
| Yonkers Rapid Transit Railway | | NYC | 1879 | 1887 | New York and Northern Railway | - |