| Name | Mark | System | From | To | Successor | Notes |
| Abbotsford and Northeastern Railroad | A&NE | CP | 1889 | 1910 | Wisconsin Central Railway | - |
| Ahnapee and Western Railway | AW, AHW | GB&W | 1890 | 1993 | Fox Valley and Western Ltd. | - |
| Alexander-Edgar Railroad | AEL | | 1899 | 1906 | | - |
| Allouez Bay Dock Company | | GN | 1903 | 1913 | Great Northern Railway | - |
| Appleton and New London Railway | | CNW | 1866 | 1875 | Milwaukee, Lake Shore and Western Railroad, Milwaukee, Lake Shore and Western Railway | - |
| Ashland Railway | | CNW | 1882 | 1885 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Ashland, Odanah and Marengo Railway | AO&M | | 1902 | 1921 | N/A | - |
| Baraboo Air Line Railroad | | CNW | 1870 | 1871 | Chicago and North Western Railway | - |
| Bayfield Harbor and Great Western Railroad | | | | | | - |
| Bayfield, Superior and Minneapolis Railway | | | | | | - |
| Bayfield Transfer Railway | | | 1883 | 1933 | N/A | - |
| Bayfield Western Railroad | | | 1898 | | | - |
| Beaver Dam and Baraboo Railroad | | MILW | 1855 | 1856 | Madison, [Fond du Lac and Michigan Railroad] | - |
| Beloit and Madison Railroad | | CNW | 1852 | 1871 | Chicago and North Western Railway | - |
| Beloit and Taycheedah Railroad | | CNW | 1848 | 1850 | Rock River Valley Union Railroad | - |
| Big Falls Railway | | | | | | - |
| Black River Railroad | | CNW | 1878 | 1880 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Burlington Northern Inc. | BN | | 1970 | 1981 | Burlington Northern Railroad | - |
| Burlington Northern Railroad | BN | | 1981 | 1996 | Burlington Northern and Santa Fe Railway | - |
| Calumet and Blue Island Railway | | | 1896 | 1897 | Chicago, Lake Shore and Eastern Railway | - |
| Cazenovia and Sauk City Railroad | | | 1909 | 1913 | Cazenovia Southern Railroad | - |
| Cazenovia Southern Railroad | | | 1913 | 1937 | N/A | - |
| Cedar Falls and Northern Railway | | CNW | 1881 | 1883 | Menomonie Railway | - |
| Central [Wisconsin Railroad] | | | 1920 | 1926 | Fairchild and Northeastern Railroad | - |
| Central Wisconsin Railroad | CWRC | | 1980 | 1985 | Wisconsin and Calumet Railroad | - |
| Chicago, Burlington and Northern Railroad | | CB&Q | 1885 | 1899 | Chicago, Burlington and Quincy Railroad | - |
| Chicago, Burlington and Quincy Railroad | CB&Q | CB&Q | 1899 | 1970 | Burlington Northern Inc. | - |
| Chicago, Burlington and Quincy Railway | | CB&Q | 1901 | 1907 | N/A | Leased the Chicago, Burlington and Quincy Railroad |
| Chicago, Fairchild & Eau Claire Railroad | CF&EC | | 1882 | 1897 | Fairchild and Northeastern Railroad | |
| Chicago, Lake Shore and Eastern Railway | | | 1897 | 1909 | Elgin, Joliet and Eastern Railway | - |
| Chicago and Lake Superior Railway | | | 1897 | | | - |
| Chicago, Madison and Northern Railroad | | | 1980 | 1982 | Central Wisconsin Railroad | - |
| Chicago, Madison and Northern Railroad | | IC | 1886 | 1903 | Illinois Central Railroad | - |
| Chicago and Milwaukee Railway | | CNW | 1863 | 1881 | Chicago, Milwaukee and North Western Railway | |
| Chicago, Milwaukee and North Western Railway | | CNW | 1881 | 1883 | Chicago and North Western Railway | - |
| Chicago, Milwaukee and St. Paul Railway | | MILW | 1874 | 1928 | Chicago, Milwaukee, St. Paul and Pacific Railroad | - |
| Chicago, Milwaukee, St. Paul and Pacific Railroad | MILW | MILW | 1928 | 1985 | The Milwaukee Road, Inc. | - |
| Chicago and North Western Railway | CNW | CNW | 1859 | 1972 | Chicago and North Western Transportation Company | - |
| Chicago and North Western Transportation Company | CNW | CNW | 1972 | 1995 | Union Pacific Railroad | - |
| Chicago, St. Paul and Fond du Lac Railroad | | CNW | 1855 | 1859 | Chicago and North Western Railway | - |
| Chicago, St. Paul and Minneapolis Railway | | CNW | 1878 | 1880 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Chicago, St. Paul, Minneapolis and Omaha Railway | CMO | CNW | 1880 | 1972 | Chicago and North Western Transportation Company | - |
| Chicago and Superior Railroad | | MILW | 1873 | 1880 | Chicago, Milwaukee and St. Paul Railway | - |
| Chicago and Tomah Railroad | | CNW | 1872 | 1880 | Milwaukee and Madison Railway | - |
| Chicago, Wisconsin and Minnesota Railroad | | CP | 1885 | 1899 | Wisconsin Central Railway | - |
| Chicago, Wisconsin and Northern Railroad | | CP | 1884 | 1888 | Chicago, Wisconsin and Minnesota Railroad | - |
| Chippewa Falls and Northern Railway | | CNW | 1881 | 1883 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Chippewa Falls and Western Railway | | CP | 1873 | 1888 | Minnesota, St. Croix and Wisconsin Railroad | - |
| Chippewa River Railroad | CVSR | | | | | - |
| Chippewa River and Menomonie Railway | | | 1883 | 1902 | Chippewa River and Northern Railway | - |
| Chippewa River and Northern Railway | | | 1902 | | | - |
| Chippewa Valley and Northern Railway | | | 1900 | | | - |
| Chippewa Valley and Northwestern Railway | | CNW | 1901 | 1904 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Chippewa Valley and Superior Railway | | MILW | 1881 | 1882 | Chicago, Milwaukee and St. Paul Railway | - |
| Connor-Flanner Railroad | | | 1927 | 1932 | N/A | - |
| Cuyuna Dock Company | | NP | 1912 | 1915 | Northern Pacific Railway | - |
| Dells and Northeastern Railway | | | 1936 | 1947 | N/A | - |
| Dixon, Rockford and Kenosha Railway | | CNW | 1864 | 1864 | Chicago and North Western Railway | - |
| Drummond and Southwestern Railway | D&SW | | 1895 | 1912 | | - |
| Dubuque, Platteville and Milwaukee Railroad | | MILW | 1867 | 1880 | Mineral Point Railroad | - |
| Duluth, Missabe and Northern Railway | DM&N | | 1915 | 1937 | Duluth, Missabe and Iron Range Railway | - |
| Duluth Short Line Railway | | NP | 1886 | 1898 | St. Paul and Duluth Railroad | - |
| Duluth, South Shore and Atlantic Railroad | | CP | 1949 | 1961 | Soo Line Railroad | - |
| Duluth, South Shore and Atlantic Railway | DS&A, DSS&A, DSA | CP | 1887 | 1949 | Duluth, South Shore and Atlantic Railroad | - |
| Duluth and Superior Bridge Company | | | 1894 | | | - |
| Duluth, Superior and Michigan Railway | | CP | 1886 | 1887 | Duluth, South Shore and Atlantic Railway | - |
| Duluth, Superior and Western Terminal Company | | GN | 1897 | 1908 | Allouez Bay Dock Company, Great Northern Railway | - |
| Duluth and Winnipeg Terminal Company | | GN | 1892 | 1897 | Duluth, Superior and Western Terminal Company | - |
| Dunbar and Wausaukee Railway | D&W | | 1892 | 1918 | Wisconsin & Northwestern Railroad | - |
| Eastern Railway of Minnesota | | GN | 1888 | 1907 | Great Northern Railway | - |
| Eastern LaFayette and Mississippi Railway | | MILW | 1871 | 1880 | Chicago, Milwaukee and St. Paul Railway | - |
| Eau Claire Railway | | CNW | 1879 | 1893 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Eau Claire and Chippewa Falls Railway | | CNW | 1881 | 1883 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Eau Claire, Chippewa Falls and Northeastern Railway | | CNW | 1902 | 1904 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Elgin, Joliet and Eastern Railway | | | 1909 | 1913 | N/A | Leased the Milwaukee, Bay View and Chicago Railroad |
| Elgin and State Line Railroad | | CNW | 1880 | 1883 | Chicago and North Western Railway | - |
| Elkhorn and Walworth Railroad | | | 1982 | 1985 | Wisconsin and Calumet Railroad | - |
| Ettrick Railroad | | | 1929 | 1937 | N/A | - |
| Ettrick and Northern Railroad | | | 1915 | 1929 | Ettrick Railroad | - |
| Fairchild and Mississippi River Railway | | CNW | 1886 | 1887 | Sault Ste. Marie and Southwestern Railway | - |
| Fairchild and North-Eastern Railway | F&NE | | 1898 | 1920 | Central Wisconsin Railroad | - |
| Fairchild and Northeastern Railroad | F&NE | | 1926 | 1929 | N/A | - |
| Fond du Lac, Amboy and Peoria Railway | | MILW | 1875 | 1883 | Chicago, Milwaukee and St. Paul Railway | - |
| Fond du Lac and Whitewater Railway | | MILW | 1874 | 1875 | Fond du Lac, Amboy and Peoria Railway | - |
| Fox Lake Railroad | | MILW | 1859 | 1904 | Chicago, Milwaukee and St. Paul Railway | - |
| Fox Lake and Wisconsin River Railroad | | MILW | 1857 | 1859 | Fox Lake Railroad | - |
| Fox River Valley Railroad | FRVR | | 1988 | 1993 | Fox Valley and Western Ltd. | - |
| Fox Valley and Western Ltd. | FVW | | 1993 | 2002 | Wisconsin Central Ltd. | - |
| Freeport, Dodgeville and Northern Railroad | | IC | 1887 | 1888 | Chicago, Madison and Northern Railroad | - |
| Galena and Southern Wisconsin Railroad | | CNW | 1857 | 1879 | Galena and Wisconsin Railroad | - |
| Galena and Wisconsin Railroad | | CNW | 1879 | 1880 | Chicago and Tomah Railroad | - |
| Galesville and Mississippi River Railroad | | CNW | 1882 | 1883 | Chicago and North Western Railway | - |
| Glenwood and Northern Railway | | | 1902 | | | - |
| Glidden & Northeastern Railroad | | | 1919 | 1927 | N/A | - |
| Glidden & Southwestern Railroad | | | 1909 | 1919 | N/A | - |
| Goodyear, Neillsville & Northern Railroad | | | 1889 | 1895 | N/A | - |
| Great Northern Railway | GN | GN | 1902 | 1970 | Burlington Northern Inc. | |
| Green Bay and Minnesota Railroad (I) | | | 1851 | 1866 | Green Bay and Lake Pepin Railway | Paper railroad. Never built due to lack of funds. Charter succeeded by GB&LP RR. |
| Green Bay and Lake Pepin Railway | | GB&W | 1866 | 1873 | Green Bay and Minnesota Railroad | - |
| Green Bay, Milwaukee and Chicago Railroad | | CNW | 1851 | 1857 | Milwaukee and Chicago Railroad | - |
| Green Bay and Minnesota Railroad (II) | | GB&W | 1873 | 1881 | Green Bay, Winona and St. Paul Railroad | - |
| Green Bay, Oshkosh, Madison and Southwestern Railroad | | CP | 1903 | 1906 | Wisconsin and Northern Railroad | - |
| Green Bay, Stevens Point and Northern Railroad | | GB&W | 1881 | 1896 | Green Bay and Western Railroad | - |
| Green Bay and Western Railroad | GB&W, GBW | GB&W | 1896 | 1993 | Fox Valley and Western Ltd. | - |
| Green Bay, Winona and St. Paul Railroad | | GB&W | 1881 | 1896 | Green Bay and Western Railroad | - |
| Hawthorne, Nebagamon and Superior Railway | HN&S | | 1898 | 1907 | N/A | - |
| Hazelhurst and Southeastern Railway | | | 1896 | | | - |
| Hiles & Eastern Railroad | | | 1905 | 1906 | | - |
| Hillsboro and Northeastern Railway | HLNE | | 1901 | 1985 | Chicago and North Western Railway | - |
| Hudson and River Falls Railway | | CNW | 1878 | 1880 | North Wisconsin Railway | - |
| Illinois Central Railroad | IC | IC | 1888 | 1972 | Illinois Central Gulf Railroad | - |
| Illinois Central Gulf Railroad | ICG | | 1972 | 1980 | Chicago, Madison and Northern Railroad | - |
| I&M Rail Link | IMRL | | 1997 | 2002 | Iowa, Chicago and Eastern Railroad | - |
| Interstate Transfer Railway | | | 1907 | 1938 | Duluth, Missabe and Iron Range Railway | - |
| Iola and Northern Railroad | | GB&W | 1893 | 1914 | Green Bay and Western Railroad | - |
| Iowa, Chicago and Eastern Railroad | ICE | | 2002 | 2008 | Dakota, Minnesota and Eastern Railroad | - |
| Iron Ridge and Mayville Railroad | | MILW | 1865 | 1878 | Fond du Lac, Amboy and Peoria Railway | - |
| Janesville, Beloit and Rockford Railway | | MILW | 1880 | 1882 | Chicago, Milwaukee and St. Paul Railway | - |
| Janesville and Evansville Railway | | CNW | 1886 | 1887 | Chicago and North Western Railway | - |
| Janesville and Southeastern Railway | | MILW | 1900 | 1901 | Chicago, Milwaukee and St. Paul Railway | - |
| Kenosha and Beloit Railroad | | CNW | 1853 | 1857 | Kenosha and Rockford Railroad | - |
| Kenosha and Rockford Railroad | | CNW | 1857 | 1857 | Kenosha, Rockford and Rock Island Railroad | - |
| Kenosha, Rockford and Rock Island Railroad | | CNW | 1864 | 1864 | Dixon, Rockford and Kenosha Railway | - |
| Kenosha, Rockford and Rock Island Railroad | | CNW | 1857 | 1857 | Kenosha and State Line Railroad | - |
| Kenosha and State Line Railroad | | CNW | 1857 | 1864 | Kenosha, Rockford and Rock Island Railroad | - |
| Kettle Moraine Scenic Railway | KMRY | MILW | 1971 | 2001 | N/A | - |
| Kewaunee, [Green Bay and Western Railroad] | KGB | GB&W | 1890 | 1969 | Green Bay and Western Railroad | - |
| Kickapoo Valley and Northern Railway | | MILW | 1889 | 1899 | Wisconsin Western Railroad | - |
| La Crosse and Milwaukee Railroad | | MILW | 1852 | 1867 | Milwaukee and St. Paul Railway | - |
| La Crosse and Onalaska Short Line Railroad | | MILW | 1888 | 1903 | Chicago, Milwaukee and St. Paul Railway | - |
| La Crosse and Southeastern Railway | | MILW | 1904 | 1933 | Chicago, Milwaukee, St. Paul and Pacific Railroad | - |
| La Crosse, Trempealeau and Prescott Railroad | | CNW | 1857 | 1877 | Chicago and North Western Railway | - |
| Lake Geneva and State Line Railway | | CNW | 1887 | 1889 | Chicago and North Western Railway | - |
| Lake Superior and Southeastern Railway | | CP | 1904 | 1908 | Wisconsin Central Railway | - |
| Lake Superior and South Western Railway | | GN | 1885 | 1888 | Eastern Railway of Minnesota | - |
| Lake Superior Terminal and Transfer Railway | LSTT | CNW/ CP/ GN/ NP | 1884 | 1987 | Burlington Northern Railroad | - |
| Laona and Northern Railway | LNO | | 1902 | 1983 | Nicolet Badger Northern Railroad | - |
| Lisbon, Necedah and Lake Superior Railway | | MILW | 1889 | 1891 | Chicago, Milwaukee and St. Paul Railway | - |
| Lone Rock – La Valle Railroad | | | 1904 | 1907 | Cazenovia and Sauk City Railroad | - |
| Madison and Beloit Railroad | | CNW | 1848 | 1850 | Rock River Valley Union Railroad | - |
| Madison, Fond du Lac and Michigan Railroad | | MILW | 1855 | 1858 | Milwaukee, Watertown and Baraboo Valley Railroad | - |
| Madison, Lodi and Baraboo Railroad | | CNW | 1864 | 1870 | Baraboo Air Line Railroad | - |
| Madison and Portage Railroad | | MILW | 1870 | 1873 | Chicago and Superior Railroad | - |
| Madison and Prairie du Chien Railroad | | MILW | 1852 | 1853 | Milwaukee and Mississippi Railroad | - |
| Manitowoc, Green Bay and North-Western Railway | | CNW | 1904 | 1909 | Chicago and North Western Railway | - |
| Manitowoc and Mississippi Railroad | | CP | 1851 | 1868 | Manitowoc and Minnesota Railroad | - |
| Manitowoc and Minnesota Railroad | | CP | 1868 | 1871 | Wisconsin Central Railroad | - |
| Manitowoc and Western Railroad | | CP | 1895 | 1895 | Milwaukee and Lake Winnebago Railroad | - |
| Manville & Eau Pleine River Railroad | | WC | 1881 | 1908 | N/A | - |
| Marathon County Railway | | | 1903 | 1928 | N/A | - |
| Marinette, Tomahawk and Western Railroad | MTW | | 1912 | 1992 | Tomahawk Railway | - |
| Marinette, Tomahawk and Western Railway | | | 1894 | 1912 | Marinette, Tomahawk and Western Railroad | - |
| Markesan and Brandon Railway | | MILW | 1882 | 1903 | Chicago, Milwaukee and St. Paul Railway | - |
| Marshfield and Southeastern Railroad | | CP | 1896 | 1901 | Wisconsin Central Railway | - |
| Mattoon Railway | | | 1895 | | | - |
| Mazomanie, Sauk City and Prairie du Sac Railroad | | MILW | 1880 | 1886 | Chicago, Milwaukee and St. Paul Railway | - |
| Menasha and Appleton Railway | | MILW | 1879 | 1880 | Milwaukee and Northern Railroad | - |
| Menominee Railway | | CNW | 1879 | 1880 | Menominee River Railroad | - |
| Menominee River Railroad | | CNW | 1880 | 1882 | Chicago and North Western Railway | - |
| Menomonie Railway | | CNW | 1879 | 1893 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Milwaukee, Bay View and Chicago Railroad | | | 1889 | 1913 | Illinois Steel Company | - |
| Milwaukee and Chicago Railroad | | CNW | 1857 | 1863 | Chicago and Milwaukee Railway | - |
| Milwaukee, Dexterville and Northern Railway | | MILW | 1884 | 1891 | Chicago, Milwaukee and St. Paul Railway | - |
| Milwaukee and Fond du Lac Railroad | | MILW | 1851 | 1853 | Milwaukee, Fond du Lac and Green Bay Railroad | - |
| Milwaukee, Fond du Lac and Green Bay Railroad | | MILW | 1853 | 1854 | La Crosse and Milwaukee Railroad | - |
| Milwaukee and Horicon Railroad | | MILW | 1852 | 1863 | Milwaukee and St. Paul Railway | - |
| Milwaukee, Lake Shore and Western Railroad | | CNW | 1872 | 1875 | Milwaukee, Lake Shore and Western Railway | - |
| Milwaukee, Lake Shore and Western Railway | | CNW | 1875 | 1893 | Chicago and North Western Railway | - |
| Milwaukee and Lake Winnebago Railroad | | CP | 1882 | 1899 | Wisconsin Central Railway | - |
| Milwaukee and Madison Railway | | CNW | 1880 | 1881 | Chicago, Milwaukee and North Western Railway | - |
| Milwaukee, Manitowoc and Green Bay Railroad | | CNW | 1870 | 1872 | Milwaukee, Lake Shore and Western Railroad | - |
| Milwaukee, Menomonee Falls and Western Railway | | MILW | 1885 | 1891 | Milwaukee and Superior Railway | - |
| Milwaukee and Mississippi Railroad | | MILW | 1850 | 1861 | Milwaukee and Prairie du Chien Railway | - |
| Milwaukee and Northern Railroad | | MILW | 1880 | 1893 | Chicago, Milwaukee and St. Paul Railway | - |
| Milwaukee and Northern Railway | | MILW | 1870 | 1880 | Milwaukee and Northern Railroad | - |
| Milwaukee and Northwestern Railway | | CNW | 1871 | 1872 | Northwestern Union Railway | - |
| Milwaukee and Prairie du Chien Railway | | MILW | 1861 | 1867 | Milwaukee and St. Paul Railway | - |
| The Milwaukee Road, Inc. | MILW | MILW | 1985 | 1986 | Soo Line Railroad | - |
| Milwaukee and St. Paul Railway | | MILW | 1863 | 1874 | Chicago, Milwaukee and St. Paul Railway | - |
| Milwaukee, Sparta and North Western Railway | | CNW | 1909 | 1912 | Chicago and North Western Railway | - |
| Milwaukee and State Line Railway | | CNW | 1905 | 1909 | Chicago and North Western Railway | - |
| Milwaukee and Superior Railroad | | MILW | 1856 | 1859 | Milwaukee and Northern Railway | - |
| Milwaukee and Superior Railway | | MILW | 1891 | 1900 | Chicago, Milwaukee and St. Paul Railway | - |
| Milwaukee and Watertown Railroad | | MILW | 1851 | 1856 | La Crosse and Milwaukee Railroad | - |
| Milwaukee, Watertown and Baraboo Valley Railroad | | MILW | 1858 | 1861 | Milwaukee and Western Railroad | - |
| Milwaukee and Waukesha Railroad | | MILW | 1847 | 1850 | Milwaukee and Mississippi Railroad | - |
| Milwaukee and Western Railroad | | MILW | 1861 | 1863 | Milwaukee and St. Paul Railway | - |
| Mineral Point Railroad | | MILW | 1852 | 1880 | Chicago, Milwaukee and St. Paul Railway | - |
| Mineral Point and Northern Railway | MP&N | | 1899 | 1930 | N/A | - |
| Minneapolis, St. Paul and Ashland Railway | | | 1894 | 1906 | N/A | - |
| Minneapolis, St. Paul and Sault Ste. Marie Railroad | SOO | CP | 1944 | 1961 | Soo Line Railroad | - |
| Minneapolis, St. Paul and Sault Ste. Marie Railway | SOO | CP | 1888 | 1944 | Minneapolis, St. Paul and Sault Ste. Marie Railroad | - |
| Minneapolis, Sault Ste. Marie and Atlantic Railway | | CP | 1883 | 1888 | Minneapolis, St. Paul and Sault Ste. Marie Railway | - |
| Minnesota, St. Croix and Wisconsin Railroad | | CP | 1884 | 1888 | Wisconsin Central Company | - |
| Minnesota and Wisconsin Railroad | | CNW | 1896 | 1902 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Minnesota and Wisconsin Railway | | CNW | 1892 | 1896 | Minnesota and Wisconsin Railroad | - |
| Miscauno and North-Western Railway | | | 1905 | 1905 | Wisconsin and Michigan Railway | - |
| Necedah and Camp Douglas Railroad | | MILW | 1874 | 1878 | Chicago, Milwaukee and St. Paul Railway | - |
| Neillsville and North Eastern Railway | | CNW | 1881 | 1884 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Nicolet Badger Northern Railroad | NBNR | | 1980 | 1994 | N/A | - |
| North Wisconsin Railway | | CNW | 1871 | 1880 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Northern Pacific Railroad | | NP | 1864 | 1896 | Northern Pacific Railway | - |
| Northern Pacific Railway | NP | NP | 1896 | 1970 | Burlington Northern Inc. | - |
| Northwestern Coal Railway | | GN | 1892 | 1953 | Great Northern Railway | - |
| Northwestern Union Railway | | CNW | 1872 | 1881 | Chicago and Milwaukee Railway | - |
| Oconto and South Western Railway | | MILW | 1889 | 1890 | Milwaukee and Northern Railroad | - |
| Oshkosh and Mississippi River Railroad | | MILW | 1866 | 1893 | Chicago, Milwaukee and St. Paul Railway | - |
| Oshkosh Transportation Company | | CNW | 1867 | 1984 | Chicago and North Western Transportation Company | - |
| Owen and Northern Railway | | CP | 1904 | 1908 | Wisconsin Central Railway | - |
| Packwaukee and Montello Railroad | | CP | 1881 | 1899 | Wisconsin Central Railway | - |
| Penokee Railroad | | CP | 1886 | 1888 | Wisconsin Central Company | - |
| Peshtigo Harbor Railroad | | | 1862 | 1895 | Wisconsin and Michigan Railway | - |
| Pine River Valley and Stevens Point Railroad | | MILW | 1872 | 1880 | Chicago, Milwaukee and St. Paul Railway | - |
| Platteville and Calamine Railroad | | MILW | 1861 | 1867 | Dubuque, Platteville and Milwaukee Railroad | - |
| Port Edwards, Centralia and Northern Railway | | CP | 1890 | 1896 | Marshfield and Southeastern Railroad | - |
| Portage, Stevens Point and Superior Railroad | | CP | 1870 | 1870 | Portage, Winnebago and Superior Railroad | - |
| Portage and Superior Railroad | | CP | 1866 | 1869 | Portage, Winnebago and Superior Railroad | - |
| Portage, Winnebago and Superior Railroad | | CP | 1869 | 1871 | Wisconsin Central Railroad | - |
| Prairie du Chien and McGregor Railway | | MILW | 1872 | 1894 | Chicago, Milwaukee and St. Paul Railway | - |
| Princeton and North Western Railway | | CNW | 1900 | 1901 | Chicago and North Western Railway | - |
| Princeton and Western Railway | | CNW | 1883 | 1912 | Milwaukee, Sparta and North Western Railway | - |
| Racine, Janesville and Mississippi Railroad | | MILW | 1852 | 1855 | Racine and Mississippi Railroad | - |
| Racine and Mississippi Railroad | | MILW | 1855 | 1868 | Western Union Railroad | - |
| Rice Lake, Dallas and Menomonie Railway | | CP | 1893 | 1900 | Minneapolis, St. Paul and Sault Ste. Marie Railway | - |
| Rice Lake and Northern Railway | | CP | 1901 | 1902 | Minneapolis, St. Paul and Sault Ste. Marie Railway | - |
| Ripon and Wolf River Railroad | | MILW | 1856 | 1863 | Milwaukee and St. Paul Railway | - |
| Robbins Railroad | | | 1898 | | | - |
| Rock River Railway | | CNW | 1880 | 1883 | Chicago and North Western Railway | - |
| Rock River Valley Union Railroad | | CNW | 1850 | 1855 | Chicago, St. Paul and Fond du Lac Railroad | - |
| Siskowit & Southern Railroad | | | 1894 | 1895 | Ashland, Siskowit & Iron River Railway | - |
| St. Cloud – Grantsburgh and Ashland Railway | | NP | 1878 | 1899 | St. Paul and Duluth Railroad | - |
| St. Croix and Chippewa Falls Railroad | | CP | 1884 | 1884 | Minnesota, St. Croix and Wisconsin Railroad | - |
| St. Croix and Duluth Railway | | | 1899 | 1908 | Washburn & Northwestern Railroad | - |
| St. Croix and Superior Railroad | | MILW | 1853 | 1857 | La Crosse and Milwaukee Railroad | - |
| St. Paul and Duluth Railroad | | NP | 1884 | 1900 | Northern Pacific Railway | - |
| St. Paul Eastern Grand Trunk Railway | | CNW | 1879 | 1913 | Chicago and North Western Railway | - |
| Sault Ste. Marie and Southwestern Railway | | CNW | 1887 | 1893 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Sheboygan and Fond du Lac Railroad | | CNW | 1861 | 1880 | Sheboygan and Western Railway | - |
| Sheboygan and Mississippi Railroad | | CNW | 1852 | 1861 | Sheboygan and Fond du Lac Railroad | - |
| Sheboygan and Western Railway | | CNW | 1880 | 1881 | Chicago, Milwaukee and North Western Railway | - |
| Southern Wisconsin Railroad | | MILW | 1852 | 1856 | Milwaukee and Mississippi Railroad | - |
| South Range Narrow Gauge Railroad | SRNG | | 1891 | 1896 | N/A | - |
| Stanley, Merrill and Phillips Railway | | | 1894 | 1899 | N/A | - |
| State Line and Union Railroad | | CNW | 1871 | 1880 | Elgin and State Line Railroad | - |
| Sugar River Valley Railroad | | MILW | 1855 | 1880 | Chicago, Milwaukee and St. Paul Railway | - |
| Superior, Balsam Lake and Southern Railway | | CP | 1900 | 1901 | Minneapolis, St. Paul and Sault Ste. Marie Railway | - |
| Superior Belt Line and Terminal Railway | | GN | 1891 | 1900 | Duluth, Superior and Western Terminal Company, Eastern Railway of Minnesota | - |
| Superior and St. Croix Railroad | | NP | 1870 | 1896 | Northern Pacific Railway | - |
| Superior Short Line Railway | | CNW | 1884 | 1895 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Superior and Southeastern Railway | | | 1920 | 1930 | | - |
| Superior Terminal and Belt Line Railway | | GN | 1890 | 1891 | Superior Belt Line and Terminal Railway | - |
| Thunder River Railroad | | | 1909 | 1927 | N/A | - |
| Tomah and Lake St. Croix Railroad | | CNW | 1863 | 1867 | West Wisconsin Railway | - |
| Tomahawk and Eastern Railway | | | 1907 | 1919 | N/A | - |
| Tony and North Eastern Railway | | | 1902 | 1903 | Minneapolis, St. Paul and Sault Ste. Marie Railway | - |
| Unity & Northwestern Railroad | | | 1893 | 1897 | N/A | - |
| Viroqua Railway | | MILW | 1878 | 1880 | Chicago, Milwaukee and St. Paul Railway | - |
| Wabeno, Otter Lake & Eastern Railroad | WOLE | | 1905 | 1930 | N/A | - |
| Washburn, Bayfield and Iron River Railway | | NP | 1895 | 1902 | Northern Pacific Railway | - |
| Washburn & Northwestern Railroad | W&NW | | 1887 | 1905 | White River Railroad | - |
| Washburn & Northwestern Railroad | W&NW | | 1902 | 1910 | N/A | - |
| Watertown and Madison Railroad | | MILW | 1853 | 1858 | Milwaukee, Watertown and Baraboo Valley Railroad | - |
| Waupaca – Green Bay Railway | | GB&W | 1907 | 1921 | Green Bay and Western Railroad | - |
| West Range Railroad | | | 1889 | 1897 | Mineral Lake & Western Railroad | - |
| West Wisconsin Railway | | CNW | 1867 | 1878 | Chicago, St. Paul and Minneapolis Railway | - |
| Western Union Railroad | | MILW | 1863 | 1900 | Chicago, Milwaukee and St. Paul Railway | - |
| Whitcomb and Morris Railway | | | 1896 | | | - |
| White River Railroad | WRRR | | 1905 | 1914 | N/A | - |
| Winnebago Railroad | | MILW | 1853 | 1866 | Oshkosh and Mississippi River Railroad | - |
| Winnebago and Superior Railroad | | CP | 1866 | 1869 | Portage, Winnebago and Superior Railroad | - |
| Winona, Alma and Northern Railway | | CB&Q | 1883 | 1885 | Chicago, Burlington and Northern Railroad | - |
| Winona Bridge Railway | | CB&Q/ GB&W | 1890 | 1985 | N/A | - |
| Wisconsin and Calumet Railroad | WICT | | 1985 | 1997 | Wisconsin and Southern Railroad | - |
| Wisconsin Central Company | | CP | 1887 | 1899 | Wisconsin Central Railway | - |
| Wisconsin Central Railroad | | CP | 1954 | 1961 | Soo Line Railroad | - |
| Wisconsin Central Railroad | | CP | 1871 | 1899 | Wisconsin Central Railway | - |
| Wisconsin Central Railway | | CP | 1897 | 1954 | Wisconsin Central Railroad | - |
| Wisconsin and Chippewa Railway | | | 1891 | 1898 | Marinette, Tomahawk and Western Railway | - |
| Wisconsin and Michigan Railroad | | MILW | 1881 | 1887 | Milwaukee and Northern Railroad | - |
| Wisconsin and Michigan Railroad | | | 1918 | 1938 | N/A | - |
| Wisconsin and Michigan Railway | WAND | | 1992 | 1995 | N/A | |
| Wisconsin and Michigan Railway | | | 1894 | 1918 | Wisconsin and Michigan Railroad | - |
| Wisconsin Midland Railroad | | MILW | 1887 | 1897 | Chicago, Milwaukee and St. Paul Railway | - |
| Wisconsin and Minnesota Railroad | | CP | 1879 | 1888 | Wisconsin Central Company | - |
| Wisconsin and Northern Railroad | W&N | CP | 1906 | 1921 | Minneapolis, St. Paul and Sault Ste. Marie Railway | - |
| Wisconsin Northern Railway | | CNW | 1896 | 1897 | Chicago and North Western Railway | - |
Wisconsin &
Northwestern Railway | W&NW | | 1906 | 1921 | N/A | - |
| Wisconsin, Pittsville and Superior Railway | | MILW | 1882 | 1891 | Chicago, Milwaukee and St. Paul Railway | - |
| Wisconsin, Ruby and Southern Railway | WRS | | 1907 | 1912 | N/A | - |
| Wisconsin and Superior Railroad | | CNW | 1856 | 1857 | Chicago, St. Paul and Fond du Lac Railroad | - |
| Wisconsin Union Railroad | | MILW | 1866 | 1872 | Milwaukee and St. Paul Railway | - |
| Wisconsin Valley Railroad | | MILW | 1871 | 1880 | Chicago, Milwaukee and St. Paul Railway | - |
| Wisconsin Western Railroad | WIWR | | 1982 | 1985 | Wisconsin and Calumet Railroad | - |
| Wisconsin Western Railroad | | MILW | 1899 | 1909 | Chicago, Milwaukee and St. Paul Railway | - |
| Wolf River Valley Railway | | CNW | 1906 | 1920 | Chicago and North Western Railway | - |
| Wolf and Wisconsin Rivers Railroad | | CNW | 1885 | 1889 | Milwaukee, Lake Shore and Western Railway | - |
| Wood County Railroad | | MILW | 1883 | 1891 | Chicago, Milwaukee and St. Paul Railway | - |
| Woodville and Southern Railway | | CNW | 1889 | 1892 | Minnesota and Wisconsin Railway | - |