| Name | Mark | System | From | To | Successor | Notes |
| Alameda and San Joaquin Railroad | | WP | 1895 | 1903 | Western Pacific Railway | |
| Alameda Belt Line | ABL | ATSF/ WP | 1925 | 2007 | N/A | |
| Albion Railroad | | | 1921 | 1930 | N/A | |
| Albion River Railroad | | NWP | 1885 | 1891 | Albion and Southeastern Railway | |
| Albion and Southeastern Railway | | NWP | 1902 | 1905 | Fort Bragg and Southeastern Railroad | |
| Almaden Branch Railroad | | SP | 1887 | 1887 | South Pacific Coast Railway | |
| Amador Branch Railroad | | SP | 1875 | 1888 | Northern Railway | |
| Amador Central Railroad | AMC | | 1908 | 1997 | Amador Foothills Railroad | |
| Amador Foothills Railroad | | | 1998 | 2004 | N/A | |
| Arcata and Mad River Railroad | AMR | | 1881 | 1985 | Eureka Southern Railroad | |
| Arcata Transportation Company | | | 1875 | 1881 | Arcata and Mad River Railroad | |
| Arizona and California Railway | | ATSF | 1903 | 1911 | California, Arizona and Santa Fe Railway | |
| Atchison, Topeka and Santa Fe Railway | ATSF | ATSF | 1901 | 1996 | Burlington Northern and Santa Fe Railway | |
| Atlantic and Pacific Railroad | | ATSF | 1866 | 1897 | Santa Fe Pacific Railroad | |
| Bakersfield and Ventura Railroad | | | 1908 | 1911 | Ventura County Railway | |
| Bakersfield and Ventura Railway | | | 1903 | 1906 | Bakersfield and Ventura Railroad | |
| Barnwell and Searchlight Railway | | ATSF | 1906 | 1911 | California, Arizona and Santa Fe Railway | |
| Bay and Coast Railroad | | SP | 1877 | 1887 | South Pacific Coast Railway | |
| Bay Point and Clayton Railroad | BP&C | | 1906 | 1946 | U.S. Navy | |
| Bear Harbor and Eel River Railroad | | | 1893 | 1921 | Abandoned | |
| Berkeley Branch Railroad | | SP | 1876 | 1888 | Northern Railway | |
| Black Diamond Coal Mining Railroad | | | 1868 | 1885 | | |
| Boca and Loyalton Railroad | | WP | 1900 | 1916 | Western Pacific Railroad | |
| Bodie Railway and Lumber Company | | | 1893 | 1906 | Mono Lake Railway and Lumber Company | |
| Bodie Railway and Lumber Company | | | 1881 | 1882 | Bodie and Benton Railway and Commercial Company | |
| Bodie and Benton Railway and Commercial Company | | | 1882 | 1890 | Bodie Railway and Lumber Company | |
| Bucksport and Elk River Railroad | | | 1884 | 1932 | Bucksport and Elk River Railway | |
| Bucksport and Elk River Railway | | | 1932 | 1952 | N/A | |
| Burlington Northern Inc. | BN | | 1970 | 1981 | Burlington Northern Railroad | |
| Burlington Northern Railroad | BN | | 1981 | 1996 | Burlington Northern and Santa Fe Railway | |
| Butte County Railroad | | SP | 1903 | 1915 | N/A | Leased the Chico and Northern Railroad |
| Butte and Plumas Railway | | WP | 1902 | 1905 | Western Pacific Railway | |
| California, Arizona and Santa Fe Railway | | ATSF | 1911 | 1963 | Atchison, Topeka and Santa Fe Railway | |
| California Central Railroad | | | 1912 | 1930 | N/A | |
| California Central Railroad | | SP | 1857 | 1868 | California and Oregon Railroad | |
| California Central Railway | | ATSF | 1887 | 1889 | Southern California Railway | |
| California Eastern Railway | | ATSF | 1895 | 1911 | California, Arizona and Santa Fe Railway | |
| California Midland Railroad | | NWP | 1902 | 1903 | San Francisco and Northwestern Railway | |
| California and Mount Diablo Railroad | | ATSF | 1880 | 1884 | California and Nevada Railroad | |
| California and Nevada Railroad | | ATSF | 1884 | 1902 | Oakland and East Side Railroad | |
| California Northeastern Railway | | SP | 1905 | 1911 | Oregon Eastern Railway | |
| California Northern Railroad | | SP | 1860 | 1881 | Northern California Railroad | |
| California and Northern Railway | | NWP | 1900 | 1904 | San Francisco and Northwestern Railway | |
| California Northwestern Railway | | NWP | 1898 | 1907 | Northwestern Pacific Railroad | |
| California and Oregon Railroad | | SP | 1865 | 1870 | Central Pacific Railroad | |
| California Pacific Railroad | | SP | 1865 | 1898 | Southern Pacific Railroad | |
| California Pacific Railroad Extension Company | | SP | 1869 | 1869 | California Pacific Railroad | |
| California, Shasta and Eastern Railway | | | 1912 | 1927 | N/A | |
| California Southern Railroad | | ATSF | 1914 | 1942 | Atchison, Topeka and Santa Fe Railway | |
| California Southern Railroad | | ATSF | 1880 | 1889 | Southern California Railway | |
| California Southern Railroad | | SP | 1870 | 1870 | Southern Pacific Railroad | |
| California Southern Extension Railroad | | ATSF | 1881 | 1882 | California Southern Railroad | |
| California Western Railroad | CWR | | 1947 | 2003 | N/A | |
| California Western Railroad and Navigation Company | CWR | | 1905 | 1947 | California Western Railroad | |
| Camino, Placerville and Lake Tahoe Railroad | CPLT | | 1911 | 1986 | N/A | |
| Carrizo Gorge Railway | CZRY | | 1997 | 2012 | Pacific Imperial Railroad | |
| Carson and Colorado Railroad | | SP | 1881 | 1892 | Carson and Colorado Railway | |
| Carson and Colorado Railway | | SP | 1892 | 1905 | Nevada and California Railway | |
| Cement, Tolenas and Tidewater Railroad | | | 1911 | 1930 | N/A | |
| Central California Railway | | SP | 1904 | 1912 | Central Pacific Railway | |
| Central Pacific Railroad | | SP | 1861 | 1899 | Central Pacific Railway | |
| Central Pacific Railway | | SP | 1899 | 1959 | Southern Pacific Company | |
| Chico and Northern Railroad | | SP | 1903 | 1912 | Central Pacific Railway | |
| Chino Valley Railway | | | 1888 | 1901 | N/A | |
| Chowchilla Pacific Railway | | SP | 1913 | 1924 | Visalia Electric Railroad | |
| Cloverdale and Ukiah Railroad | | NWP | 1886 | 1889 | San Francisco and North Pacific Railway | |
| Coal Fields Railway | | | 1920 | 1935 | N/A | |
| Coast Line Railway | | SP | 1905 | 1917 | Southern Pacific Railroad | |
| Colusa Railroad | | | 1885 | 1886 | Colusa and Lake Railroad | |
| Colusa and Hamilton Railroad | | SP | 1911 | 1917 | Southern Pacific Railroad | |
| Colusa and Lake Railroad | | | 1886 | 1915 | N/A | |
| Corona and Santa Fe Railway | | ATSF | 1926 | 1942 | Atchison, Topeka and Santa Fe Railway | |
| Coronado Railroad | | SP | 1886 | 1908 | San Diego Southern Railway | |
| Crescent City Railway | | UP | 1906 | 1915 | Riverside, Rialto and Pacific Railroad | |
| Death Valley Railroad | | | 1914 | 1931 | N/A | |
| Diamond and Caldor Railway | | | 1904 | 1952 | N/A | |
| Eel River and Eureka Railroad | | NWP | 1882 | 1903 | San Francisco and Northwestern Railway | |
| Elsinore, Pomona and Los Angeles Railway | | ATSF | 1895 | 1899 | Southern California Railway | |
| Eureka and Klamath River Railroad | | NWP | 1896 | 1907 | Northwestern Pacific Railroad | |
| Eureka Southern Railroad | EUKA | | 1984 | 1992 | North Coast Railroad | |
| Feather River Railway | | | 1939 | 1966 | N/A | |
| Felton and Pescadero Railroad | | SP | 1883 | 1887 | South Pacific Coast Railway | |
| Ferris and Lakeview Railway | | ATSF | 1898 | 1911 | California, Arizona and Santa Fe Railway | |
| Fernley and Lassen Railway | | SP | 1909 | 1912 | Central Pacific Railway | |
| Folsom and Placerville Railroad | | SP | 1876 | 1877 | Sacramento and Placerville Railroad | |
| Fort Bragg and Southeastern Railroad | | NWP | 1903 | 1907 | Northwestern Pacific Railroad | |
| Freeport Railroad | | | 1863 | 1865 | N/A | |
| Fresno County Railway | | ATSF | 1905 | 1911 | California, Arizona and Santa Fe Railway | |
| Fullerton and Richfield Railway | | ATSF | 1910 | 1911 | California, Arizona and Santa Fe Railway | |
| Fulton and Guerneville Railroad | | NWP | 1877 | 1877 | San Francisco and North Pacific Railroad | |
| Goose Lake and Southern Railway | | SP | 1908 | 1912 | Central Pacific Railway | |
| Great Northern Railway | GN | GN | 1930 | 1970 | Burlington Northern Inc. | |
| Great Western Railway of Colorado | GWR | | 1986 | 1987 | Great Western Railway of Oregon | |
| Great Western Railway of Oregon | GWR | | 1987 | 1997 | Lake County Railroad | |
| Hanford and Summit Lake Railway | | SP | 1910 | 1917 | Southern Pacific Railroad | |
| Harbor Belt Line Railroad | HBL | | 1929 | 1998 | Pacific Harbor Line, Inc. | |
| Hetch Hetchy Railroad | | | 1915 | 1949 | N/A | |
| Hetch Hetchy and Yosemite Valleys Railway of California | | | 1900 | 1943 | N/A | |
| Holton Interurban Railway | HI | SP | 1903 | 1985 | Southern Pacific Transportation Company | |
| Howard Terminal Railway | HT | | 1917 | | Part of Port of Oakland Railroad | |
| Hueneme, Malibu and Port Los Angeles Railway | . | | . | | . | |
| Humboldt Railroad | | NWP | 1901 | | Northwestern Pacific Railroad | |
| Imperial and Gulf Railway | | SP | 1902 | 1905 | Inter-California Railway | |
| Indian Valley Railroad | | | 1916 | 1938 | N/A | |
| Indian Valley Railway | | WP | 1902 | 1905 | Western Pacific Railway | |
| Inter-California Railway | | SP | 1904 | 1935 | Southern Pacific Company | |
| Ione and Eastern Railroad | | | 1904 | 1908 | Amador Central Railroad | |
| Iron Mountain Railway | | | 1895 | 1927 | N/A | |
| Kings Lake Shore Railroad | | | 1917 | 1934 | N/A | |
| Kings River Railway | | ATSF | 1909 | 1911 | California, Arizona and Santa Fe Railway | |
| Klamath Lake Railroad | | | 1901 | 1913 | Siskiyou Electric Light and Power Company | |
| Lake County Railroad | LCR | | 1997 | | | Still exists as a lessor of the Lake Railway |
| Lake Tahoe Railway and Transportation Company | | SP | 1898 | 1927 | Southern Pacific Company | |
| Laton and Western Railroad | | ATSF | 1910 | 1942 | California, Arizona and Santa Fe Railway | |
| Loma Prieta Railroad | | SP | 1882 | 1884 | Pajaro and Santa Cruz Railroad | |
| Long Beach Railroad | | SP | 1887 | 1888 | Southern Pacific Railroad | |
| Long Beach, Whittier and Los Angeles County Railroad | | SP | 1887 | 1888 | Southern Pacific Railroad | |
| Los Angeles and Glendale Railroad | | UP | 1887 | 1888 | Los Angeles and Glendale Railway | |
| Los Angeles and Glendale Railway | | UP | 1888 | 1891 | Los Angeles Terminal Railway | |
| Los Angeles and Independence Railroad | | SP | 1875 | 1888 | Southern Pacific Railroad | |
| Los Angeles, Pasadena and Glendale Railway | | UP | 1889 | 1891 | Los Angeles Terminal Railway | |
| Los Angeles and Salt Lake Railroad | | UP | 1916 | 1987 | Union Pacific Railroad | - |
| Los Angeles and San Diego Railroad | | SP | 1876 | 1888 | Southern Pacific Railroad | - |
| Los Angeles and San Gabriel Valley Railroad | | ATSF | 1883 | 1887 | California Central Railway | - |
| Los Angeles and San Pedro Railroad | | SP | 1868 | 1874 | Southern Pacific Railroad | - |
| Los Angeles and Santa Monica Railroad | | ATSF | 1886 | 1887 | California Central Railway | - |
| Los Angeles Terminal Railway | | UP | 1890 | 1901 | San Pedro, Los Angeles and Salt Lake Railroad | - |
| Ludlow and Southern Railway | | | 1902 | 1931 | N/A | - |
| Marin and Napa Railroad | | NWP | 1886 | 1889 | San Francisco and North Pacific Railway | - |
| Marysville Railroad | | SP | 1867 | 1868 | California and Oregon Railroad | - |
| Marysville and Susanville Railroad | | WP | 1904 | 1905 | Western Pacific Railway | - |
| McCloud River Railroad | MR | | 1897 | 1992 | McCloud Railway | - |
| Mill Valley and Mount Tamalpais Scenic Railway | | | 1896 | 1913 | Mount Tamalpais and Muir Woods Railway | - |
| Minarets and Western Railway | | | 1921 | 1932 | N/A | - |
| Minkler Southern Railway | | ATSF | 1913 | 1942 | Atchison, Topeka and Santa Fe Railway | - |
| Modesto Interurban Railway | | | 1909 | 1993 | Modesto and Empire Traction Company | - |
| Modesto Terminal Company | | | 1920 | 1938 | Modesto Interurban Railway | - |
| Modoc Northern Railroad | MNRR | | 2005 | 2009 | Union Pacific Railroad | - |
| Modoc Northern Railway | | SP | 1908 | 1912 | Central Pacific Railway | - |
| Mojave Northern Railroad | | | 1914 | | | Still exists as a private carrier subsidiary of Cemex |
| Monterey Railroad | | SP | 1880 | 1888 | Southern Pacific Railroad | - |
| Monterey Extension Railroad | | SP | 1888 | 1888 | Southern Pacific Railroad | - |
| Monterey and Salinas Valley Railroad | | SP | 1874 | 1879 | Monterey Railroad | - |
| Mount Tamalpais and Muir Woods Railway | | | 1913 | 1930 | N/A | - |
| Napa Valley Railroad | | SP | 1864 | 1869 | California Pacific Railroad Extension Company | - |
| National City and Otay Railway | | SP | 1887 | 1908 | San Diego Southern Railway | - |
| Nevada and California Railway | | SP | 1905 | 1912 | Central Pacific Railway | - |
| Nevada and California Railroad | | SP | 1884 | 1893 | Nevada–California–Oregon Railway | - |
| Nevada–California–Oregon Railway | | SP | 1888 | 1945 | Central Pacific Railway | - |
| Nevada County Narrow Gauge Railroad | | | 1874 | 1943 | N/A | - |
| Nevada and Oregon Railroad | | SP | 1881 | 1884 | Nevada and California Railroad | - |
| Nevada Southern Railway | | ATSF | 1892 | 1895 | California Eastern Railway | - |
| Newport Wharf and Lumber Company | | SP | 1889 | 1893 | Santa Ana and Newport Railway | - |
| North Coast Railroad | NCRR | | 1992 | 1996 | Northwestern Pacific Railroad | - |
| North Pacific Coast Railroad | | NWP | 1871 | 1902 | North Shore Railroad | - |
| North Pacific Coast Railroad Extension Company | | NWP | 1882 | 1885 | North Pacific Coast Railroad | - |
| North Shore Railroad | | NWP | 1902 | 1907 | Northwestern Pacific Railroad | - |
| North Western Railroad of California | | NWP | 1885 | 1892 | North Pacific Coast Railroad | - |
| Northern Railway | | SP | 1871 | 1898 | Southern Pacific Railroad | - |
| Northern California Railroad | | SP | 1884 | 1889 | Northern California Railway | - |
| Northern California Railway | | SP | 1888 | 1898 | Southern Pacific Railroad | - |
| Northwestern Pacific Railroad | NWP | | 1996 | 2001 | Northwestern Pacific Railway | - |
| Northwestern Pacific Railroad | NWP | NWP | 1907 | 1992 | Southern Pacific Transportation Company | - |
| Northwestern Pacific Railway | NWP | | 2001 | 2001 | Northwestern Pacific Railroad | - |
| Northwestern Pacific Railway | | NWP | 1906 | 1907 | Northwestern Pacific Railroad | - |
| Oakdale Western Railway | | ATSF | 1904 | 1911 | California, Arizona and Santa Fe Railway | - |
| Oakland and East Side Railroad | | ATSF | 1902 | 1911 | California, Arizona and Santa Fe Railway | - |
| Oakland Terminal Railroad | | ATSF/ WP | 1935 | 1943 | Oakland Terminal Railway | - |
| Oakland Township Railroad | | SP | 1881 | 1887 | South Pacific Coast Railway | - |
| Ocean Shore Railroad | | | 1911 | 1920 | N/A | - |
| Ocean Shore Railway | | | 1905 | 1911 | Ocean Shore Railroad | - |
| Oregon Eastern Railway | | SP | 1911 | 1912 | Central Pacific Railway | - |
| Oregon and Eureka Railroad | | | 1903 | 1911 | N/A | Leased the Eureka and Klamath River Railroad and Humboldt Railroad |
| Otay Railway | | SP | 1887 | 1888 | National City and Otay Railway | |
| Outer Harbor Terminal Railway | | | 1927 | 1955 | N/A | |
| Pacific Coast Railroad | | | 1882 | 1882 | Pacific Coast Railway | |
| Pacific Coast Railway | | | 1882 | 1941 | N/A | All PCRY right of way in Santa Maria Valley absorbed by competitor Santa Maria Valley Railroad |
| Pacific Electric Railway | PE | SP | 1901 | 1965 | Southern Pacific Company | Electric until 1961 |
| Pacific Southwestern Railroad | | SP | 1922 | 1924 | Southern Pacific Company | |
| Pajaro and Santa Cruz Railroad | | SP | 1884 | 1888 | Southern Pacific Railroad | |
| Pajaro Valley Railroad | | | 1890 | 1897 | Pajaro Valley Consolidated Railroad | |
| Pajaro Valley Consolidated Railroad | | | 1897 | 1928 | N/A | |
| Pajaro Extension Railway | | | 1897 | 1897 | Pajaro Valley Consolidated Railroad | |
| Palmdale Railroad | | | 1888 | 1893 | N/A | |
| Parr Terminal Railroad | PRT | | 1950 | 2002 | Richmond Pacific Railroad | |
| Pasadena Railway | | UP | 1887 | 1892 | Los Angeles Terminal Railway | |
| Patterson and Western Railroad | | | 1915 | 1921 | N/A | |
| Placerville and Lake Tahoe Railway | | | 1904 | 1911 | Camino, Placerville and Lake Tahoe Railroad | |
| Placerville and Sacramento Valley Railroad | | SP | 1862 | 1869 | Sacramento and Placerville Railroad | |
| Port Railroads, Inc. | PRI | | 1973 | 1996 | San Joaquin Valley Railroad | |
| Porterville Northeastern Railway | | SP | 1910 | 1934 | Southern Pacific Company | |
| Quincy and Eastern Railroad | | | 1908 | 1909 | Quincy Western Railway | |
| Quincy Western Railway | | | 1909 | 1917 | Quincy Railroad | |
| Ramona and San Bernardino Railroad | | SP | 1888 | 1888 | Southern Pacific Railroad | |
| Randsburg Railway | | ATSF | 1897 | 1911 | California, Arizona and Santa Fe Railway | |
| Redondo Beach Railway | | ATSF | 1888 | 1889 | Southern California Railway | |
| Richmond Belt Railway | | ATSF / SP | 1902 | 1932 | Atchison, Topeka and Santa Fe Railway, Southern Pacific Company | |
| Riverside, Rialto and Pacific Railroad | | UP | 1915 | 1917 | Los Angeles and Salt Lake Railroad | |
| Riverside, Santa Ana and Los Angeles Railway | | ATSF | 1885 | 1887 | California Central Railway | |
| Sacramento Northern Railway | SN | WP | 1921 | 1987 | Western Pacific Railroad | Electric until 1946 |
| Sacramento and Oakland Railway | | WP | 1903 | 1903 | Western Pacific Railway | |
| Sacramento and Placerville Railroad | | SP | 1877 | 1888 | Northern Railway | |
| Sacramento and San Francisco Railroad | | SP | 1864 | 1865 | California Pacific Railroad | |
| Sacramento Southern Railroad | | SP | 1903 | 1912 | Central Pacific Railway | |
| Sacramento Valley Railroad | | SP | 1852 | 1877 | Sacramento and Placerville Railroad | |
| Sacramento Valley and Eastern Railway | | | 1906 | 1927 | N/A | |
| San Bernardino and Eastern Railway | | ATSF | 1890 | 1892 | Southern California Railway | |
| San Bernardino and Los Angeles Railway | | ATSF | 1886 | 1887 | California Central Railway | |
| San Bernardino and San Diego Railway | | ATSF | 1886 | 1887 | California Central Railway | |
| San Bernardino Valley Railway | | ATSF | 1887 | 1887 | California Central Railway | |
| San Diego and Arizona Railway | | SP | 1906 | 1933 | San Diego and Arizona Eastern Railway | |
| San Diego and Arizona Eastern Railway | SDAE | SP | 1933 | | | Still exists as a lessor of the Carrizo Gorge Railway and San Diego and Imperial Valley Railroad |
| San Diego and Arizona Eastern Transportation Company | SDAE | | 1979 | 1984 | San Diego and Imperial Valley Railroad | |
| San Diego Central Railroad | | ATSF | 1886 | 1887 | California Central Railway | |
| San Diego and Cuyamaca Railway | | SP | 1909 | 1912 | San Diego and South Eastern Railway | |
| San Diego and Cuyamaca Railway | | SP | 1887 | 1888 | San Diego, Cuyamaca and Eastern Railway | |
| San Diego, Cuyamaca and Eastern Railway | | SP | 1888 | 1909 | San Diego and Cuyamaca Railway | |
| San Diego and South Eastern Railway | | SP | 1912 | 1917 | San Diego and Arizona Railway | |
| San Diego Southern Railway | | SP | 1908 | 1912 | San Diego and South Eastern Railway | |
| San Francisco and Alameda Railroad | | SP | 1863 | 1870 | San Francisco, Oakland and Alameda Railroad | |
| San Francisco, Alameda and Stockton Railroad | | SP | 1863 | 1864 | San Francisco and Alameda Railroad | |
| San Francisco Bay Railroad | | SP | 1868 | 1869 | Western Pacific Railroad | |
| San Francisco Belt Railroad | SFB | | 1969 | 1993 | N/A | |
| San Francisco and Colorado River Railroad | | SP | 1883 | 1887 | South Pacific Coast Railway | |
| San Francisco and Eureka Railway | | NWP | 1903 | 1907 | Northwestern Pacific Railroad | |
| San Francisco and Humboldt Bay Railroad | | NWP | 1868 | 1869 | San Francisco and North Pacific Railroad | |
| San Francisco and Marysville Railroad | | SP | 1857 | 1865 | California Pacific Railroad | |
| San Francisco and Napa Railway | | SP | 1903 | 1911 | Southern Pacific Railroad | |
| San Francisco and North Pacific Railroad | | NWP | 1869 | 1889 | San Francisco and North Pacific Railway | |
| San Francisco and North Pacific Railway | | NWP | 1888 | 1907 | Northwestern Pacific Railroad | |
| San Francisco and Northwestern Railway | | NWP | 1903 | 1907 | Northwestern Pacific Railroad | |
| San Francisco and Oakland Railroad | | SP | 1861 | 1870 | San Francisco, Oakland and Alameda Railroad | |
| San Francisco, Oakland and Alameda Railroad | | SP | 1870 | 1870 | Central Pacific Railroad | |
| San Francisco and San Joaquin Valley Railway | | ATSF | 1895 | 1901 | Atchison, Topeka and Santa Fe Railway | |
| San Francisco and San Jose Railroad | | SP | 1860 | 1870 | Southern Pacific Railroad | |
| San Francisco and San Rafael Railroad | | NWP | 1882 | 1889 | San Francisco and North Pacific Railway | |
| San Francisco, Tamalpais and Bolinas Railway | | NWP | 1889 | 1892 | North Pacific Coast Railroad | |
| San Francisco Terminal Railway and Ferry Company | | WP | 1902 | 1903 | Western Pacific Railway | |
| San Gabriel Valley Rapid Transit Railway | | SP | 1887 | 1894 | Southern Pacific Railroad | |
| San Jacinto Valley Railway | | ATSF | 1887 | 1887 | California Central Railway | |
| San Joaquin and Eastern Railroad | SJ&E | | 1912 | 1933 | N/A | |
| San Joaquin and Sierra Nevada Railroad | | SP | 1882 | 1888 | Northern Railway | |
| San Joaquin Valley Railroad | | SP | 1891 | 1893 | Southern Pacific Railroad | |
| San Joaquin Valley Railroad | | SP | 1868 | 1870 | Central Pacific Railroad | |
| San Joaquin Valley and Yosemite Railroad | | SP | 1886 | 1888 | Southern Pacific Railroad | |
| San Jose and Almaden Railroad | | SP | 1886 | 1888 | Southern Pacific Railroad | |
| San Juan Pacific Railway | | | 1907 | 1912 | California Central Railroad | |
| San Luis Obispo Railroad | | | 1873 | 1875 | San Luis Obispo and Santa Maria Valley Railroad | |
| San Luis Obispo and Santa Maria Valley Railroad | | | 1875 | 1882 | Pacific Coast Railway | |
| San Pablo and Tulare Railroad | | SP | 1871 | 1888 | Southern Pacific Railroad | |
| San Pablo and Tulare Extension Railroad | | SP | 1887 | 1888 | Southern Pacific Railroad | |
| San Pedro, Los Angeles and Salt Lake Railroad | SLR | UP | 1901 | 1916 | Los Angeles and Salt Lake Railroad | |
| San Rafael and San Quentin Railroad | | NWP | 1869 | | | |
| San Ramon Valley Railroad | | SP | 1888 | 1888 | Southern Pacific Railroad | |
| Santa Ana Railroad | | SP | 1889 | 1892 | Newport Wharf and Lumber Company | |
| Santa Ana and Newport Railway | | SP | 1892 | 1899 | Southern Pacific Railroad | |
| Santa Ana and Westminster Railway | | SP | 1890 | 1899 | Santa Ana and Newport Railway | |
| Santa Clara and Pajaro Valley Railroad | | SP | 1868 | 1870 | Southern Pacific Railroad | |
| Santa Cruz Railroad | | SP | 1873 | 1881 | Pajaro and Santa Cruz Railroad | |
| Santa Cruz and Felton Railroad | | SP | 1874 | 1887 | South Pacific Coast Railway | |
| Santa Fe and Los Angeles Harbor Railway | | ATSF | 1922 | 1942 | Atchison, Topeka and Santa Fe Railway | |
| Santa Fe Pacific Railroad | | ATSF | 1897 | 1902 | Atchison, Topeka and Santa Fe Railway | |
| Santa Fe and Santa Monica Railway | | ATSF | 1892 | 1892 | Southern California Railway | |
| Santa Fe Terminal Company of California | | ATSF | 1899 | 1912 | Atchison, Topeka and Santa Fe Railway | |
| Santa Rosa and Carquinez Railroad | | SP | 1887 | 1888 | | - |
| Saratoga and Almaden Railroad | | | 1884 | 1905 | N/A | |
| Shingle Springs and Placerville Railroad | | SP | 1887 | 1888 | Northern Railway | |
| Sierra Railroad | SERA | | 1935 | 2003 | Sierra Northern Railway | |
| Sierra Railway of California | SRYC | | 1897 | 1937 | Sierra Railroad | |
| Sierra and Mohawk Railway | | SP | 1911 | 1915 | Sierra and Mohawk Railway | - |
| Sierra Valley & Mohawk Railway | | SP | 1885 | 1895 | Sierra Valley Railroad | - |
| Sierra Valley Railroad | | SP | 1895 | 1909 | Sierra and Mohawk Railway | - |
| Sonoma County Railroad | | NWP | 1868 | 1868 | San Francisco and Humboldt Bay Railroad | - |
| Sonoma and Marin Railroad | | NWP | 1875 | 1877 | San Francisco and North Pacific Railroad | - |
| Sonoma and Santa Rosa Railroad | | NWP | 1881 | 1885 | Sonoma Valley Railroad | - |
| Sonoma Valley Railroad | | NWP | 1878 | 1889 | San Francisco and North Pacific Railway | - |
| Sonoma Valley Prismoidal Railway | | NWP | 1875 | 1878 | Sonoma Valley Railroad | - |
| South Pacific Coast Railroad | | SP | 1876 | 1887 | South Pacific Coast Railway | - |
| South Pacific Coast Railway | | SP | 1887 | 1937 | Southern Pacific Company | - |
| South San Francisco Belt Railway | | SP | 1907 | 1945 | Southern Pacific Company | - |
| Southern California Railway | | ATSF | 1889 | 1906 | Atchison, Topeka and Santa Fe Railway | - |
| Southern California Motor Road | | SP | 1887 | 1895 | Southern Pacific Railroad | - |
| Southern Pacific Company | SP | SP | 1885 | 1969 | Southern Pacific Transportation Company | - |
| Southern Pacific Railroad | | SP | 1865 | 1955 | Southern Pacific Company | - |
| Southern Pacific Railroad Extension Company | | SP | 1888 | 1888 | Southern Pacific Railroad | - |
| Southern Pacific Branch Railroad | | SP | 1872 | 1873 | Southern Pacific Railroad | - |
| Southern Pacific Branch Railway | | SP | 1886 | 1888 | Southern Pacific Railroad | - |
| Southern Pacific Transportation Company | SP | SP | 1969 | 1998 | Union Pacific Railroad | - |
| State Belt Railroad | | | 1873 | 1969 | San Francisco Belt Railroad | - |
| Stockton and Beckwith Pass Railway | | WP | 1902 | 1903 | Western Pacific Railway | - |
| Stockton and Copperopolis Railroad | | SP | 1865 | 1888 | Southern Pacific Railroad | - |
| Stockton and Ione Railroad | | | 1873 | 1875 | N/A | - |
| Stockton and Tulare Railroad | | SP | 1887 | 1888 | Southern Pacific Railroad | - |
| Stockton and Visalia Railroad | | SP | 1869 | 1877 | Stockton and Copperopolis Railroad | - |
| Sugar Pine Railway | | | 1903 | 1922 | N/A | - |
| Sunset Railroad | | ATSF/ SP | 1900 | 1912 | Sunset Railway | - |
| Sunset Railway | SUN | ATSF/ SP | 1912 | | | Still exists as a joint subsidiary of the BNSF Railway and Union Pacific Railroad, leased to the San Joaquin Valley Railroad |
| Sunset Western Railway | | ATSF/ SP | 1909 | 1912 | Sunset Railway | - |
| Ten Mile Railroad | | | | | | Fort Bragg |
| Tidewater and Southern Railroad | | WP | 1910 | 1912 | Tidewater Southern Railway | - |
| Tidewater Southern Railway | TSO, TS | WP | 1912 | 1987 | Western Pacific Railroad | - |
| Tidewater and Southern Transit Company | | WP | 1912 | 1912 | Tidewater Southern Railway | - |
| Tonopah and Tidewater Railroad | | | 1904 | 1940 | N/A | - |
| Vaca Valley Railroad | | SP | 1869 | 1870 | Vaca Valley and Clear Lake Railroad | - |
| Vaca Valley and Clear Lake Railroad | | SP | 1877 | 1888 | Northern Railway | - |
| Ventura County Railway | VCY | | 1911 | | | Still exists as a lessor of the Ventura County Railroad |
| Ventura and Ojai Valley Railroad | | SP | 1896 | 1899 | Southern Pacific Railroad | - |
| Visalia Railroad | | SP | 1874 | 1899 | Southern Pacific Railroad | - |
| Visalia Electric Railroad | VE | SP | 1904 | 1992 | Southern Pacific Transportation Company | Electric until 1944 |
| Visalia and Tulare Railroad | | | 1887 | 1900 | N/A | - |
| West Side and Mendocino Railroad | | SP | 1886 | 1888 | Northern Railway | - |
| Western Nevada Railroad | | SP | 1879 | 1880 | Nevada and Oregon Railroad | - |
| Western Pacific Railroad | WP | WP | 1916 | 1987 | Union Pacific Railroad | - |
| Western Pacific Railroad | | SP | 1862 | 1870 | Central Pacific Railroad | - |
| Western Pacific Railway | | WP | 1903 | 1916 | Western Pacific Railroad | - |
| Winters and Ukiah Railway | | SP | 1887 | 1888 | Northern Railway | - |
| Woodland, Capay and Clear Lake Railroad | | SP | 1887 | 1888 | Northern Railway | - |
| Yolo Shortline Railroad | YSLR | | 1991 | 2003 | Sierra Northern Railway | - |
| Yosemite Short Line Railway | | | 1905 | 1917 | N/A | - |
| Yosemite Valley Railroad | | | 1902 | 1935 | Yosemite Valley Railway | - |
| Yosemite Valley Railway | | | 1934 | 1945 | N/A | - |
| Yreka Railroad | | | 1888 | 1935 | Yreka Western Railroad | - |
| Yuba Railroad | | SP | 1862 | 1869 | California and Oregon Railroad | - |
