Railroad companies grew, divided, merged, changed names, shrank, and disappeared depending upon need, competition, success, jurisdiction challenges and legal regulations. Some companies, especially the narrow gauge lines, arose to service a particular industry and disappeared when the lumber or mineral resource was exhausted. Here is a list of companies which have operated in or through New Mexico over the years.
Note: many company names started out as "Railroad" but later changed to "Railway", and some similar company names reflect reorganizations. More than a few companies were created but never actually operated, usually becoming absorbed into a new company.
- Alamogordo and Sacramento Mountain Railway (nicknamed the "Cloud-Climbing Railroad")
- Albuquerque Eastern Railway
- Amtrak
- Arizona & Colorado Railroad
- Arizona Eastern Railroad
- Arizona & New Mexico Railway
- Atchison, Topeka & Santa Fe Railroad, later "Railway" (AT&SF, "The Santa Fe Railway")
- Atlantic & Pacific Railroad
- Burlington Northern & Santa Fe Railroad
- Burro Mountain Railroad
- Cerrillos Coal Railroad
- Chicago, Rock Island & Choctaw Railway
- Chicago, Rock Island & El Paso Railway: The Golden State Route
- Chicago, Rock Island & Pacific Railway
- Cimarron & Northwestern Railway
- Clifton & Lordsburg Railway
- Colorado & Southern Railway
- Cuba Extension Railroad
- Cumbres & Toltec Scenic Railroad
- Dawson Railway
- Denver & Rio Grande Railroad (nicknamed "The Chile Line")
- Denver & Rio Grande Western Railroad
- Denver, Texas & Fort Worth Railroad
- Denver, Texas & Gulf Railroad
- Eastern Railway of New Mexico
- El Paso & Northeastern Railroad (nicknamed the "White Oaks Railroad")
- El Paso & Rock Island Railway Company
- El Paso & Southwestern Railroad
- Elkhart & Santa Fe Railway
- Fort Worth & Denver City Railway
- Hanover Railroad
- Lordsburg & Hachita Railroad
- Missouri Pacific Railroad
- Moreno and Rio Hondo Railroad (proposed)
- New Mexican and Pacific Railroad Company
- New Mexican Railroad
- New Mexico and Southern Pacific Railroad (later "Railway")
- New Mexico Central Railroad
- New Mexico Gateway Railroad
- New Mexico Midland Railway
- New Mexico Railroad Company
- Pecos Northern Railroad
- Pecos Valley Railroad
- Pecos Valley & Northeastern Railway
- Rail Runner Express
- Rio Grande, Mexico & Pacific Railroad
- Rio Grande & Pagosa Springs Railroad
- Rio Grande & Santa Fe Railroad
- Rio Grande & Southwestern Railroad
- Rocky Mountain & Santa Fe Railway
- Santa Fe, Albuquerque & Pacific Railroad
- Santa Fe Central Railway
- Santa Fe Northern Railroad
- Santa Fe Northwestern Railway
- Santa Fe Pacific Railroad
- Santa Fe Railway (popular name for the AT&SF)
- Santa Fe, Raton & Des Moines Railroad
- Santa Fe, San Juan & Northern Railroad
- Santa Fe Southern Railroad
- Santa Rita Railroad
- Silver City, Deming & Pacific Railroad
- Silver City & Northern Railroad
- Silver City, Pinos Altos & Mogollon Railroad
- Southern Pacific Railroad Company of New Mexico
- Southern Pacific Transportation Company
- Southwestern Railroad of New Mexico
- St. Louis, Rocky Mountain & Pacific Railway
- St. Louis Southwestern Railway
- Texas - New Mexico Railway
- Texas, Santa Fe & Northern Railroad
- Tierra Amarilla Southern Railroad
- Tucumcari & Memphis Railroad
- Union Pacific, Denver & Gulf Railway
- United States Potash Railroad
- White Oaks Railroad (popular name for the El Paso & Northeastern)