| Name | Mark | System | From | To | Successor | Notes |
| Alder Creek Railway | | | 1912 | 1918 | N/A | - |
| Boise City Railway and Terminal Company | | UP | 1893 | 1910 | Oregon Short Line Railroad | - |
| Boise, Nampa and Owyhee Railway | | UP | 1896 | 1907 | Idaho Northern Railway | - |
| Burlington Northern Inc. | BN | | 1970 | 1981 | Burlington Northern Railroad | - |
| Burlington Northern Railroad | BN | | 1981 | 1996 | Burlington Northern and Santa Fe Railway | - |
| Camas Prairie RailNet | CSP | | 1998 | 2004 | Great Northwest Railroad | - |
| Camas Prairie Railroad | CSP | NP/ UP | 1909 | 1998 | Camas Prairie RailNet | - |
| Canyon Creek Railroad | | NP | 1887 | 1888 | Coeur d'Alene Railway and Navigation Company | - |
| Central Idaho Railroad | | UP | 1910 | 1914 | Oregon Short Line Railroad | - |
| Chicago, Milwaukee and Puget Sound Railway | | MILW | 1909 | 1912 | Chicago, Milwaukee and St. Paul Railway | - |
| Chicago, Milwaukee and St. Paul Railway | | MILW | 1912 | 1928 | Chicago, Milwaukee, St. Paul and Pacific Railroad | - |
| Chicago, Milwaukee and St. Paul Railway of Idaho | | MILW | 1906 | 1908 | Chicago, Milwaukee and St. Paul Railway of Washington | - |
| Chicago, Milwaukee and St. Paul Railway of Washington | | MILW | 1908 | 1909 | Chicago, Milwaukee and Puget Sound Railway | - |
| Chicago, Milwaukee, St. Paul and Pacific Railroad | MILW | MILW | 1928 | 1980 | St. Maries River Railroad, Union Pacific Railroad | - |
| Clearwater Short Line Railway | | NP | 1898 | 1914 | Northern Pacific Railway | - |
| Clearwater Valley Railroad | | UP | 1898 | 1916 | Oregon–Washington Railroad and Navigation Company | - |
| Coeur d'Alene Railway and Navigation Company | | NP | 1886 | 1897 | Northern Pacific Railway | - |
| Coeur d'Alene and Pend d'Oreille Railway | | UP | 1910 | 1941 | Spokane International Railroad | - |
| Columbia and Palouse Railroad | | UP | 1882 | 1910 | Oregon Railroad and Navigation Company | - |
| Craig Mountain Railway | | | 1921 | 1965 | N/A | - |
| Craig Mountain Lumber Company's Railway | | | 1909 | 1921 | Craig Mountain Railway | - |
| Gilmore and Pittsburgh Railroad | | NP | 1907 | 1939 | N/A | - |
| Great Northern Railway | GN | GN | 1890 | 1970 | Burlington Northern Inc. | - |
| Idaho Central Railway | | UP | 1886 | 1889 | Oregon Short Line and Utah Northern Railway | - |
| Idaho Northern Railroad | | UP | 1906 | 1910 | Oregon–Washington Railroad and Navigation Company | - |
| Idaho Northern Railway | | UP | 1897 | 1912 | Oregon Short Line Railroad | - |
| Idaho Southern Railroad | | | 1908 | 1916 | N/A | - |
| Idaho and Washington Northern Railroad | | MILW | 1907 | 1916 | Chicago, Milwaukee and St. Paul Railway | - |
| Idaho and Western Railway | | MILW | 1909 | 1912 | Chicago, Milwaukee and Puget Sound Railway | - |
| Intermountain Railway | | | 1907 | 1935 | N/A | - |
| Kootenai Valley Railway | | GN | 1898 | 1913 | Great Northern Railway | - |
| Lake Creek and Coeur d'Alene Railroad | | UP | 1906 | 1910 | Oregon–Washington Railroad and Navigation Company | - |
| Lewiston, Nezperce and Eastern Railroad | | | 1915 | 1924 | N/A | - |
| Malad Valley Railroad | | UP | 1902 | 1910 | Oregon Short Line Railroad | - |
| Milner and North Side Railroad | | | 1907 | 1915 | N/A | - |
| Minidoka and Southwestern Railroad | | UP | 1904 | 1910 | Oregon Short Line Railroad | - |
| Nezperce Railroad | NEZP | | 1945 | 1983 | N/A | - |
| Nez Perce and Idaho Railroad | | | 1917 | 1946 | Nezperce Railroad | - |
| Nez Perce and Idaho Railroad | | | 1908 | 1915 | Lewiston, Nezperce and Eastern Railroad | - |
| Northern Pacific Railroad | | NP | 1864 | 1896 | Northern Pacific Railway | - |
| Northern Pacific Railway | NP | NP | 1896 | 1970 | Burlington Northern Inc. | - |
| Ohio Match Company Railway | | SI | 1903 | 1944 | Converted into roads. | - |
| Oregon Railroad and Navigation Company | | UP | 1896 | 1910 | Oregon–Washington Railroad and Navigation Company | - |
| Oregon Railway and Navigation Company | | UP | 1884 | 1896 | Oregon Railroad and Navigation Company | - |
| Oregon Short Line Railroad | | UP | 1897 | 1987 | Union Pacific Railroad | - |
| Oregon Short Line Railway | | UP | 1882 | 1889 | Oregon Short Line and Utah Northern Railway | - |
| Oregon Short Line and Utah Northern Railway | | UP | 1889 | 1897 | Oregon Short Line Railroad | - |
| Oregon–Washington Railroad and Navigation Company | | UP | 1910 | 1987 | Union Pacific Railroad | - |
| Oregon, Washington and Idaho Railroad | | UP | 1903 | 1910 | Oregon–Washington Railroad and Navigation Company | - |
| Pacific and Idaho Northern Railway | P&IN | UP | 1899 | 1936 | Oregon Short Line Railroad | - |
| Palouse River and Coulee City Railroad | PCC | | 1996 | 2006 | Washington and Idaho Railway | - |
| Payette Valley Railroad | | UP | 1906 | 1914 | Oregon Short Line Railroad | - |
| Payette Valley Extension Railroad | | UP | 1910 | 1914 | Oregon Short Line Railroad | - |
| St. Anthony Railroad | | UP | 1899 | 1910 | Oregon Short Line Railroad | - |
| Salmon River Railroad | | UP | 1901 | 1910 | Oregon Short Line Railroad | - |
| Salt Lake and Idaho Railroad | | UP | 1909 | 1914 | Oregon Short Line Railroad | - |
| San Francisco, Idaho and Montana Railway | | UP | 1905 | 1909 | Oregon Short Line Railroad | - |
| Spokane, Coeur d'Alene and Palouse Railway | | GN | 1926 | 1943 | Great Northern Railway | Electric until 1941 |
| Spokane Falls and Idaho Railroad | | NP | 1886 | 1898 | Northern Pacific Railway | - |
| Spokane International Railroad | SI | UP | 1941 | 1987 | Union Pacific Railroad | - |
| Spokane International Railway | | UP | 1905 | 1941 | Spokane International Railroad | - |
| Spokane and Palouse Railway | | NP | 1886 | 1898 | Northern Pacific Railway | - |
| Utah Northern Railroad | | UP | 1872 | 1878 | Utah and Northern Railway | - |
| Utah and Northern Railway | | UP | 1878 | 1889 | Oregon Short Line and Utah Northern Railway | - |
| Wallace and Sunset Railroad | | NP | 1890 | 1898 | Northern Pacific Railway | - |
| Washington and Idaho Railroad | | UP | 1886 | 1896 | Oregon Railroad and Navigation Company | - |
| Washington, Idaho and Montana Railway | WIM | MILW | 1905 | 1980 | Burlington Northern Inc. | - |
| Weiser, Idaho and Spokane Railway | | UP | | 1899 | Pacific and Idaho Northern Railway | - |
| Yellowstone Park Railroad | | UP | 1905 | 1910 | Oregon Short Line Railroad | - |