Caltrain is the one continuously operating Commuter Rail Line west of Chicago. It is the direct predecessor of the Southern Pacific's Peninsula Commute Service. The line operates hourly or better 7 days a week between San Francisco and San Jose. Service south of San Jose to Gilroy is limited to 3 peak direction rush hour trips. During rush hours, all trains are either Limited, making limited stops (some make all stops either north or south of Redwood City with timed 5 minute transfers for passengers wanting local service) or Baby Bullet Express trains. Every station always has service every 60 minutes or better.

Rolling Stock: Caltrain uses 93 Nippon-Sharyo Galley Cars (purchased in 1985 or 2000) and 25 Bombardier BiLevel Cars (purchased in 2002 and 2008), the two fleets cannot mix, all trains are Galley cars or BiLevel cars. Trains operate in push-pull mode and are powered by 23 F40PH and 6 MP36PH Locomotives. Locomotives are always at the San Jose/Gilroy-bound end; running southbound in pull-mode and northbound in push-mode.

History: Caltrain's has its direct origins as the Southern Pacific's Peninsula Commute Service that was the outcome of the local passengers trains that have operated continuously ever since the San Francisco peninsula has had a railroad starting with its completion in 1863. Steam Locomotives were used extremely late in commute service until January 1957. Amtrak's 1971 takeover of passenger trains only covered intercity rail service. This required the Southern Pacific to continue operating it's last commuter service, the San Francisco to San Jose Commuter Trains. In 1977 the SP petitioned to discontinue the service and the state of California stepped in and subsidies began in 1980.

In 1985, with new Galley Cars and F40PH Locomotives purchased (still in use today), the state renamed the operation CalTrain. The Peninsula Joint Powers Board formed in 1987 to manage the line (with representatives from the three counties the line passes through). Unlike BART or any of the other transit systems in the region, Caltrain has no dedicated tax revenue, this makes Caltrain's budget a yearly struggle. In 1991 the corridor between San Jose and San Francisco was purchased from the SP by the state. On July 1, 1992 Amtrak was chosen as the operator for the service, ending Southern Pacific's 122 year reign as the continuous operator of passenger train service along the corridor. This same day a few trains a day were extended south to Gilroy (the line here is still owned and dispatched by the UP that absorbed the SP in 1996). A rebranding effort in July 1997 gave the line its current name of Caltrain.

In the early 2000s Caltrain underwent a number of capacity improvements. This included the CTX Caltrain Express program between 2002 and 2004 that discontinued weekend service over this timeframe for the construction of passing sidings at Brisbane and Sunnyvale along with a new Centralized Train Control system. Over Memorial Day Weekend 2012 TransitAmerica services (a subsidiary of Herzog Transit Systems, also the operator of the Altamont Commuter Express), took over operations from Amtrak.

Fare Payment: Caltrain operates a zonal fare system with 6 total zones (4 zones are the core of the corridor between San Francisco and San Jose). On September 22, 2003 Caltrain discontinued the conductors punch with the full installation of TVMs at all stations and the introduction of POP (Proof-of-Payment). This requires all passengers to have a ticket and valid fare payment before boarding. Those that don't can no longer just buy a ticket on board with a small surcharge but are fare evading with a maximum fine of $250. This new fare system also introduced Day Passes (priced at two one-way tickets). On Caltrain, conductors both control train movements and are fare inspectors with at least one fare inspection normally occurring along every trip between San Francisco and San Jose. On April 23, 2010 (after various pilots) TransLink Cards (that were renamed Clipper Cards that same year), the San Francisco Bay Interagency fare card, began acceptance on Caltrain. All Caltrain stations have readers and riders must Tag On before boarding and Tag Off after exiting or else are subject to paying the full fare for the entire corridor to Gilroy. Today all 8 ride multi-trip tickets and monthly passes can only be purchased on a clipper card. Those riders paying with cash at a TVM pay 25¢ more for a one-way fare. A flaw of Clipper on Caltrain is Caltrain's TVMs can't issue or reload Clipper Cards. Passengers wanting multi-ride tickets can only purchase them at retailers, special Clipper Vending Machines and other transit agencies ticket offices.