| Allensworth Station (CNL) Flag stop |
| Anaheim Regional Transportation Intermodal Center (ANA) |
| Antioch–Pittsburg Station (ACA) |
| Auburn Station (California) (ARN) |
| Bakersfield Station (Amtrak) (BFD) |
| Barstow Harvey House (BAR) |
| Berkeley Station (California) (BKY) |
| Burbank Airport–South Station (BUR) |
| Camarillo Station (CML) |
| Carpinteria Station (CPN) |
| Chatsworth Station (CWT) |
| Chico Station (CIC) |
| Colfax Station (COX) |
| Corcoran Station (COC) |
| Davis Station (California) (DAV) |
| Denair Station (TRK) |
| Dunsmuir Station (DUN) |
| El Garces Intermodal Transportation Facility (Needles) (NDL) |
| Emeryville Station (EMY) |
| Fairfield–Vacaville Station (FFV) |
| Fremont Station (FMT) |
| Fullerton Transportation Center (FUL) |
| Glendale Transportation Center (GDL) |
| Goleta Station (GTA) |
| Grover Beach Station (GVB) |
| Guadalupe Station (GUA) |
| Hanford Station (HNF) |
| Hayward Station (Amtrak) (HAY) |
| Irvine Transportation Center (IRV) |
| Lodi Transit Station (LOD) |
| Lompoc–Surf Station (LPS) |
| Madera Station (Amtrak) (MDR) |
| Martinez Station (MTZ) |
| Merced Station (Amtrak) (MCD) |
| Modesto Station (MOD) |
| Moorpark Station (MPK) |
| Oakland Coliseum Station (OAC) |
| Oakland – Jack London Square Station (OKJ) |
| Oceanside Transit Center (OSD) |
| Old Town Transit Center (San Diego) (OLT) |
| Ontario Station (Amtrak) (ONA) |
| Oxnard Transit Center (OXN) |
| Palm Springs Station (PSN) |
| Paso Robles Station (PRB) |
| Pomona Station (California) (POS) |
| Redding Station (California) (RDD) |
| Richmond Station (California) (RIC) |
| Riverside–Downtown Station (RIV) |
| Robert J. Cabral Station (Stockton) (SKT) |
| Rocklin Station (RLN) |
| Roseville Station (California) (RSV) |
| Sacramento Valley Station (SAC) |
| Salinas Station (SNS) |
| San Bernardino Santa Fe Depot (SNB) |
| San Clemente Pier Station (SNP) |
| San Joaquin Street Station (SKN) |
| San Jose Diridon Station (SJC) |
| San Juan Capistrano Station (SNC) |
| San Luis Obispo Station (SLO) |
| Santa Ana Regional Transportation Center (SNA) |
| Santa Barbara Station (SBA) |
| Santa Clara Transit Center (SCC) |
| Santa Clara – Great America Station (GAC) |
| Santa Fe Depot (San Diego) (SAN) |
| Santa Fe Passenger Depot (Fresno, California) (FNO) |
| Simi Valley Station (SIM) |
| Solana Beach Station (SOL) |
| Suisun–Fairfield Station (SUI) |
| Truckee Station (TRU) |
| Union Station (Los Angeles) (LAX) |
| Van Nuys Station (VNC) |
| Ventura Station (VEC) |
| Victor Valley Transportation Center (VRV) |
| Wasco Station (WAC) |
