| Name | Mark | System | From | To | Successor | Notes |
| Atchison, Lincoln and Columbus Railroad | | CB&Q | 1871 | 1871 | Atchison and Nebraska Railroad | - |
| Atchison and Nebraska Railroad | | CB&Q | 1871 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Atchison, Topeka and Santa Fe Railway | ATSF | ATSF | 1890 | 1996 | Burlington Northern and Santa Fe Railway | - |
| Brandon Corporation | BRAN | | 1978 | 2006 | Brandon Railroad | - |
| Brownville, Fort Kearney (aka. Kearny) and Pacific Railroad | | CB&Q | 1867 | 1875 | Nebraska Railway | - |
| Burlington and Missouri River Railroad in Nebraska | | CB&Q | 1869 | 1880 | Chicago, Burlington and Quincy Railroad | - |
| Burlington Northern Inc. | BN | | 1970 | 1981 | Burlington Northern Railroad | - |
| Burlington Northern Railroad | BN | | 1981 | 1996 | Burlington Northern and Santa Fe Railway | - |
| Burlington and Southwestern Railway | | CB&Q | 1869 | 1870 | Atchison and Nebraska Railroad | - |
| Chicago, Burlington and Quincy Railroad | CB&Q | CB&Q | 1880 | 1970 | Burlington Northern Inc. | - |
| Chicago, Burlington and Quincy Railway | | CB&Q | 1901 | 1907 | N/A | Leased the Chicago, Burlington and Quincy Railroad |
| Chicago Great Western Railroad | | CGW | 1909 | 1941 | Chicago Great Western Railway | - |
| Chicago Great Western Railway | CGW | CGW | 1941 | 1968 | Chicago and North Western Railway | - |
| Chicago Great Western Railway | | CGW | 1903 | 1909 | Chicago Great Western Railroad | - |
| Chicago, Iowa and Kansas Railroad | | CB&Q | 1883 | 1884 | Chicago, Nebraska and Kansas Railroad | - |
| Chicago, Kansas and Nebraska Railroad | | RI | 1886 | 1886 | Chicago, Kansas and Nebraska Railway | - |
| Chicago, Kansas and Nebraska Railway | | RI | 1886 | 1891 | Chicago, Rock Island and Pacific Railway | - |
| Chicago, Kansas and Western Railroad | | ATSF | 1888 | 1890 | Atchison, Topeka and Santa Fe Railway | - |
| Chicago, Milwaukee and St. Paul Railway | | MILW | 1890 | 1928 | Chicago, Milwaukee, St. Paul and Pacific Railroad | - |
| Chicago, Milwaukee, St. Paul and Pacific Railroad | MILW | MILW | 1928 | 1982 | N/A | - |
| Chicago, Nebraska and Kansas Railroad | | CB&Q | 1884 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Chicago and North Western Railway | CNW | CNW | 1901 | 1972 | Chicago and North Western Transportation Company | - |
| Chicago and North Western Transportation Company | CNW | CNW | 1972 | 1995 | Union Pacific Railroad | - |
| Chicago, Rock Island and Pacific Railroad | RI, ROCK | | 1947 | 1980 | Union Pacific Railroad | - |
| Chicago, Rock Island and Pacific Railway | RI | RI | 1888 | 1948 | Chicago, Rock Island and Pacific Railroad | - |
| Chicago, St. Paul, Minneapolis and Omaha Railway | CMO | CNW | 1881 | 1972 | Chicago and North Western Transportation Company | - |
| Covington, Columbus and Black Hills Railroad | | CNW | 1875 | 1879 | Sioux City and Nebraska Railroad | - |
| Fillmore Western Railway | FWRY | | 1996 | 1999 | N/A | - |
| Fremont, Elkhorn and Missouri Valley Railroad | | CNW | 1869 | 1903 | Chicago and North Western Railway | - |
| Grand Island, Hastings and Southeastern Railroad | | UP | 1896 | 1897 | St. Joseph and Grand Island Railway | - |
| Grand Island and Marysville Railroad | | UP | 1885 | 1885 | St. Joseph and Grand Island Railroad | - |
| Grand Island and Wyoming Central Railroad | | CB&Q | 1886 | 1897 | Chicago, Burlington and Quincy Railroad | - |
| Hastings and Grand Island Railroad | | UP | 1879 | 1880 | St. Joseph and Western Railroad | - |
| Hastings and Northwestern Railroad | | UP | 1912 | 1917 | Union Pacific Railroad | - |
| Illinois Central Railroad | IC | IC | 1899 | 1972 | Illinois Central Gulf Railroad | - |
| Illinois Central Gulf Railroad | ICG | | 1972 | 1985 | Chicago Central and Pacific Railroad | - |
| Inter State Bridge and Street Railway Company | | IC | 1890 | 1892 | Omaha Bridge and Terminal Railway Company | - |
| Kansas City and Beatrice Railroad | | MP | 1889 | 1894 | Kansas City Northwestern Railroad | - |
| Kansas City Northwestern Railroad | | | 1917 | 1919 | Kansas City Northwestern Railway | - |
| Kansas City Northwestern Railroad | | MP | 1893 | 1910 | Missouri Pacific Railway | - |
| Kansas City Northwestern Railway | | | 1925 | 1925 | N/A | - |
| Kansas City and Omaha Railroad | | CB&Q | 1886 | 1896 | Kansas City and Omaha Railway | - |
| Kansas City and Omaha Railway | | CB&Q | 1896 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Kansas City, Wyandotte and Northwestern Railroad | | MP | 1889 | 1894 | Kansas City Northwestern Railroad | - |
| Kansas and Nebraska Railway | | UP | 1876 | 1877 | St. Joseph and Western Railroad | - |
| Kearney and Black Hills Railway | | UP | 1889 | 1898 | Union Pacific Railroad | - |
| Lincoln and Black Hills Railroad | | CB&Q | 1887 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Lincoln and North Western Railroad | | CB&Q | 1879 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Midland Pacific Railway | | CB&Q | 1868 | 1875 | Nebraska Railway | - |
| Missouri Pacific Railroad | MP | MP | 1917 | 1997 | Union Pacific Railroad | - |
| Missouri Pacific Railroad in Nebraska | | MP | 1917 | 1956 | Missouri Pacific Railroad | - |
| Missouri Pacific Railway | | MP | 1882 | 1917 | Kansas City Northwestern Railroad, Missouri Pacific Railroad in Nebraska | - |
| Missouri Pacific Railway of Nebraska | | MP | 1881 | 1882 | Missouri Pacific Railway | - |
| Missouri Valley and Blair Railway and Bridge Company | | CNW | 1882 | 1920 | Chicago and North Western Railway | - |
| Nebraska Railway | | CB&Q | 1875 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Nebraska and Colorado Railroad | | CB&Q | 1883 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Nebraska, Kansas and Colorado RailNet | NKCR | | 1996 | 2005 | Nebraska Kansas Colorado Railway | - |
| Nebraska Southern Railway | | MP | 1886 | 1910 | Missouri Pacific Railway | - |
| Nebraska and Western Railway | | CB&Q | 1889 | 1891 | Sioux City, O'Neill and Western Railway | - |
| Nebraska, Wyoming and Western Railroad | | CB&Q | 1899 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| North-Eastern Nebraska Railroad | | CNW | 1888 | 1888 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Northern Nebraska Air Line Railroad | | CNW | 1867 | 1868 | Sioux City and Pacific Railroad | - |
| Omaha Belt Railway | | MP | 1883 | 1910 | Missouri Pacific Railway | - |
| Omaha Bridge and Terminal Railway Company | | IC | 1892 | 1946 | Illinois Central Railroad | - |
| Omaha, Niobrara and Black Hills Railroad | | UP | 1879 | 1886 | Omaha and Republican Valley Railway | - |
| Omaha and North Platte Railroad | | CB&Q | 1886 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Omaha and Northern Nebraska Railway | | CNW | 1878 | 1880 | Sioux City and Nebraska Railroad | - |
| Omaha and Northwestern Railroad | | CNW | 1869 | 1878 | Omaha and Northern Nebraska Railway | - |
| Omaha and Republican Valley Railroad | | UP | 1876 | 1886 | Omaha and Republican Valley Railway | - |
| Omaha and Republican Valley Railway | | UP | 1886 | 1898 | Union Pacific Railroad | - |
| Omaha and South Western Railroad | | CB&Q | 1869 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Omaha Southern Railway | | MP | 1890 | 1910 | Missouri Pacific Railway | - |
| Oxford and Kansas Railroad | | CB&Q | 1887 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Pacific Railway in Nebraska | | MP | 1887 | 1910 | Missouri Pacific Railway | - |
| Randolph and Northeastern Nebraska Railroad | | CNW | 1890 | 1890 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Republican Valley Railroad | | CB&Q | 1878 | 1888 | Chicago, Burlington and Quincy Railroad | - |
| Republican Valley and Kansas Railroad | | CB&Q | 1885 | 1886 | Republican Valley, Kansas and Southwestern Railroad | - |
| Republican Valley, Kansas and Southwestern Railroad | | CB&Q | 1886 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Republican Valley and Wyoming Railroad | | CB&Q | 1887 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| Rock Island Omaha Terminal Railway | | RI | 1914 | 1948 | Chicago, Rock Island and Pacific Railroad | - |
| St. Joseph and Denver City Railroad | | UP | 1866 | 1876 | Kansas and Nebraska Railway | - |
| St. Joseph and Grand Island Railroad | | UP | 1885 | 1897 | Grand Island, Hastings and Southeastern Railroad | - |
| St. Joseph and Grand Island Railway | SJGI | UP | 1897 | | | - |
| St. Joseph and Iowa Railroad | | RI | 1886 | 1888 | Chicago, Rock Island and Pacific Railway | - |
| St. Joseph and Western Railroad | | UP | 1877 | 1885 | Grand Island and Marysville Railroad | - |
| St. Paul and Sioux City Railroad | | CNW | 1880 | 1881 | Chicago, St. Paul, Minneapolis and Omaha Railway | - |
| Sioux City Bridge Company | | CNW | 1889 | 1956 | Chicago and North Western Railway | - |
| Sioux City and Nebraska Railroad | | CNW | 1879 | 1883 | Chicago, St. Paul, Minneapolis and Omaha Railway, St. Paul and Sioux City Railroad | - |
| Sioux City, O'Neill and Western Railway | | CB&Q | 1891 | 1899 | Sioux City and Western Railway | - |
| Sioux City and Pacific Railroad | | CNW | 1868 | 1901 | Chicago and North Western Railway | - |
| Sioux City and Western Railway | | CB&Q | 1899 | 1908 | Chicago, Burlington and Quincy Railroad | - |
| South Omaha Terminal Railway | SOT | | 1927 | 1978 | Brandon Corporation | - |
| South Omaha and Western Railroad | | UP | 1905 | 1908 | Union Pacific Railroad | - |
| Union Pacific Railroad | | UP | 1862 | 1880 | Union Pacific Railway | - |
| Union Pacific Railway | | UP | 1880 | 1897 | Union Pacific Railroad | - |
| Union Stock Yards Company of Omaha | | | 1883 | 1927 | South Omaha Terminal Railway | - |