| Name | Mark | System[nb 1] | From | To | Successor | Notes |
|---|
| Alamogordo and Sacramento Mountain Railway | | SP | 1898 | 1937 | El Paso and Southwestern Railroad | |
| Albuquerque Eastern Railway | | ATSF | 1901 | 1908 | New Mexico Central Railroad | |
| Arizona and Colorado Railroad | | SP | 1904 | 1910 | Arizona Eastern Railroad | |
| Arizona Eastern Railroad | | SP | 1904 | 1955 | Southern Pacific Company | |
| Arizona and New Mexico Railway | | SP | 1883 | 1935 | El Paso and Southwestern Railroad | |
| Atchison, Topeka and Santa Fe Railroad | | ATSF | 1878 | 1895 | Atchison, Topeka and Santa Fe Railway | |
| Atchison, Topeka and Santa Fe Railway | ATSF | ATSF | 1895 | 1996 | Burlington Northern and Santa Fe Railway | |
| Atlantic and Pacific Railroad | | ATSF | 1866 | 1897 | Santa Fe Pacific Railroad | |
| Burlington Northern Railroad | BN | | 1981 | 1996 | Burlington Northern and Santa Fe Railway | |
| Burro Mountain Railroad | | SP | 1909 | 1934 | N/A | |
| Cerrillos Coal Railroad | | ATSF | 1892 | 1901 | Atchison, Topeka and Santa Fe Railway | |
| Chicago, Rock Island and Choctaw Railway | | RI | 1903 | 1903 | Chicago, Rock Island and El Paso Railway | |
| Chicago, Rock Island and El Paso Railway | | RI | 1900 | 1910 | Chicago, Rock Island and Pacific Railway |
| Chicago, Rock Island and Pacific Railroad | RI, ROCK | RI | 1948 | 1980 | St. Louis Southwestern Railway | |
| Chicago, Rock Island and Pacific Railway | RI | RI | 1910 | 1947 | Chicago, Rock Island and Pacific Railroad | |
| Cimarron and Northwestern Railway | | | 1907 | 1930 | N/A |
| Clifton and Lordsburg Railway | | SP | 1883 | 1883 | Arizona and New Mexico Railway | |
| Colorado and Southern Railway | C&S, CS | CB&Q | 1898 | 1981 | Burlington Northern Railroad | |
| Cuba Extension Railroad | | | 1923 | 1927 | Santa Fe Northern Railroad | |
| Dawson Railway | | SP | 1901 | 1955 | Southern Pacific Company |
| Denver and Rio Grande Railroad | | DRGW | 1886 | 1921 | Denver and Rio Grande Western Railroad |
| Denver and Rio Grande Railway | | DRGW | 1870 | 1886 | Denver and Rio Grande Railroad |
| Denver and Rio Grande Western Railroad | D&RG, D&RGW, DRGW | DRGW | 1920 | 1970 | Cumbres and Toltec Scenic Railroad |
| Denver, Texas and Fort Worth Railroad | | CB&Q | 1887 | 1890 | Union Pacific, Denver and Gulf Railway |
| Eastern Railway of New Mexico | | ATSF | 1902 | 1912 | Atchison, Topeka and Santa Fe Railway |
| El Paso and Northeastern Railway | | SP | 1897 | 1937 | El Paso and Southwestern Railroad |
| El Paso and Rock Island Railway | | SP | 1900 | 1955 | Southern Pacific Company |
| El Paso and Southwestern Company | | SP | 1908 | 1924 | El Paso and Southwestern Railroad |
| El Paso and Southwestern Railroad | | SP | 1902 | 1955 | Southern Pacific Company |
| Fort Worth and Denver Railway | FWD | CB&Q | 1981 | 1982 | Burlington Northern Railroad |
| Hanover Railroad | | ATSF | 1899 | 1900 | Atchison, Topeka and Santa Fe Railway |
| Lordsburg and Hachita Railroad | | SP | 1901 | 1911 | Arizona and New Mexico Railway |
| Missouri Pacific Railroad | MP | MP | 1978 | 1989 | Texas – New Mexico Railroad |
| New Mexican Railroad | | ATSF | 1882 | 1899 | Atchison, Topeka and Santa Fe Railway |
| New Mexican Railway Company | Unknown | Unknown | 1860 | 1865? | Unknown | Incorporated Feb 2, 1860;Memorial... in Relation to the Pacific Railroad - May 21, 1860 |
| New Mexico Central Railroad | | ATSF | 1908 | 1918 | New Mexico Central Railway |
| New Mexico Central Railway | | ATSF | 1918 | 1972 | Atchison, Topeka and Santa Fe Railway |
| New Mexico Gateway Railroad | NMGR | | 2001 | 2006 | N/A |
| New Mexico Midland Railway | | | 1904 | 1931 | none, route abandoned[1] | hauled coal from Carthage to San Antonio, NM[1] |
| New Mexico and Southern Pacific Railroad | | ATSF | 1878 | 1899 | Atchison, Topeka and Santa Fe Railway | |
| Pecos Northern Railroad | | ATSF | 1890 | 1890 | Pecos Valley Railway | |
| Pecos Valley Railroad | | ATSF | 1890 | 1890 | Pecos Valley Railway | |
| Pecos Valley Railway | | ATSF | 1890 | 1898 | Pecos Valley and Northeastern Railway | |
| Pecos Valley and Northeastern Railway | | ATSF | 1898 | 1907 | Eastern Railway of New Mexico | |
| Rio Grande Eastern Railway | | | 1923 | 1931 | | ServedHagan from nearSan Felipe[2] |
| Rio Grande, Mexico and Pacific Railroad | | ATSF | 1880 | 1899 | Atchison, Topeka and Santa Fe Railway | |
| Rio Grande, Mexico and Pacific Railroad Extension Company | | ATSF | 1881 | 1881 | Rio Grande, Mexico and Pacific Railroad | |
| Rio Grande and Pagosa Springs Railroad | | | 1895 | 1914 | N/A | |
| Rio Grande and Santa Fe Railroad | | DRGW | 1895 | 1908 | Denver and Rio Grande Railroad | |
| Rio Grande and Southwestern Railroad | | DRGW | 1903 | 1924 | N/A | |
| Rocky Mountain and Santa Fe Railway | | ATSF | 1915 | 1943 | Atchison, Topeka and Santa Fe Railway | |
| St. Louis, Rocky Mountain and Pacific Railway | | ATSF | 1905 | 1915 | Rocky Mountain and Santa Fe Railway | |
| St. Louis Southwestern Railway | SSW | SP | 1980 | 1997 | Union Pacific Railroad | |
| Santa Fe, Albuquerque and Pacific Railroad | | ATSF | 1900 | 1901 | Santa Fe Central Railway | |
| Santa Fe Central Railway | | ATSF | 1901 | 1908 | New Mexico Central Railroad | |
| Santa Fe Northwestern Railway | | | 1920 | 1941 | N/A | |
| Santa Fe Northern Railroad | | | 1927 | 1928 | Santa Fe, San Juan and Northern Railroad | |
| Santa Fe Pacific Railroad | | ATSF | 1897 | 1902 | Atchison, Topeka and Santa Fe Railway | |
| Santa Fe, Raton and Des Moines Railroad | | | 1906 | 1914 | N/A | Operated bySanta Fe, Raton and Eastern Railroad |
| Santa Fe, Raton and Eastern Railroad | | ATSF | 1906 | 1924 | Rocky Mountain and Santa Fe Railway | |
| Santa Fe, San Juan and Northern Railroad | | | 1928 | 1941 | N/A | |
| Santa Fe Southern Railway (19th-century "Chili Line") | | DRGW | 1889 | 1895 | Rio Grande and Santa Fe Railroad | |
| Santa Fe Southern Railway (21st century) | | SFS | 1992 | 2014 | N/A | |
| Santa Rita Railroad | | ATSF | 1897 | 1900 | Atchison, Topeka and Santa Fe Railway | |
| Silver City, Deming and Pacific Railroad | | ATSF | 1882 | 1899 | Atchison, Topeka and Santa Fe Railway | |
| Silver City and Northern Railroad | | ATSF | 1891 | 1899 | Atchison, Topeka and Santa Fe Railway | |
| Southern Pacific Railroad | | SP | 1879 | 1955 | Southern Pacific Company | |
| Southern Pacific Company | SP | SP | 1885 | 1969 | Southern Pacific Transportation Company | |
| Southern Pacific Transportation Company | SP | SP | 1969 | 1998 | Union Pacific Railroad | |
| Southwestern Railroad of New Mexico | | SP | 1901 | 1902 | El Paso and Southwestern Railroad | |
| Texas–New Mexico Railway | TNM | MP | 1927 | 1978 | Missouri Pacific Railroad | |
| Texas, Santa Fe and Northern Railroad | | DRGW | 1880 | 1884 | Santa Fe Southern Railway | |
| Tierra Amarilla Southern Railroad | | DRGW | 1892 | 1902 | Denver and Rio Grande Railroad | |
| Tucumcari and Memphis Railway | | RI | 1909 | 1910 | Chicago, Rock Island and El Paso Railway | |
| Union Pacific, Denver and Gulf Railway | | CB&Q | 1890 | 1898 | Colorado and Southern Railway | |