The Peninsula Commute, also known as the Southern Pacific Peninsula or just Peninsula, was the common name for commuter rail service between San Jose and San Francisco on the San Francisco Peninsula. This service ran as a private, for-profit enterprise beginning in 1863. Due to operating losses, the Southern Pacific Railroad (SP) petitioned to discontinue the service in 1977. Subsidies were provided through Caltrans in 1980 to continue service, and it was renamed Caltrain in 1985.

Since 1863 the San Francisco Peninsula, the series of towns (and later, cities) between San Francisco and San Jose, has been served by a railroad. The San Francisco and San Jose Railroad first provided freight and passenger service, followed by its successor, the Southern Pacific, and then briefly by Caltrans and finally by a regional Joint Powers Board which runs today's passenger trains.

Although a line had been proposed in the past, construction on the railroad between San Francisco and San Jose was started in 1860 "by a group of local capitalists of more than ordinary energy and resources" under the auspices of the San Francisco and San Jose Railroad (SF&SJ), and completed in 1863. The Central Pacific Railroad transferred its rights for the construction of the right-of-way between San Jose and Sacramento to the Western Pacific Railroad (WPRR, which was founded by the same members that had founded the SF&SJ) in late 1862.

In December 1865, the Southern Pacific Railroad Company (SP) was incorporated to build a rail line between San Francisco and San Diego. By the end of 1868, it was revealed the Big Four of the Central Pacific consisting of Stanford, Huntington, Hopkins, and Crocker had a controlling interest in the SF&SJ and SP, and the SF&SJ, SP, the Santa Clara and Pajaro Valley Railroad, and the California Southern were folded into a consolidated Southern Pacific Railroad on October 12, 1870.

Under Southern Pacific the line was double tracked in 1904, and multiple cutoffs were built over a period ending in 1910. The first of these, the Bayshore Cutoff, opened in 1907 and rerouted the line through a series of five tunnels built along the shoreline of the San Francisco Bay Area. This saved approximately three miles and seventeen minutes compared to the prior route, which veered to the west around San Bruno Mountain. The Bayshore Cutoff also eliminated the use of helper engines to bring trains over the mountain. The second, the Mayfield Cutoff, opened in 1908 to provide service to western Santa Clara Valley cities such as Los Altos and Los Gatos. The third, the Dumbarton Cutoff, opened in 1910 and included the first bridge across the San Francisco Bay Area, between Newark and Menlo Park, saving many miles to Oakland and Sacramento compared to the prior route through San Jose and Santa Clara.

The Peninsula Electric Railroad was incorporated around the same time the Dumbarton Cutoff project was launched, and it was suspected that it was controlled by Southern Pacific in preparation for a quad-track expansion, as it was laying a route parallel with the Southern Pacific. As envisioned in 1909 from plans for the Peninsula Electric, SP announced that it would investigate the electrification of its Peninsula Commute line in September 1921, promising better and more frequent service. Just a few days later, SP cited excessive post-war inflation, taxation, and competition from publicly funded highways as factors making electrification neither "practicable or desirable". Similarly, plans to eliminate all at-grade crossings were announced in 1909, but not carried to completion. As Southern Pacific's franchise to operate on 4th Street in San Jose was ending, it elected to build a diversion track to the west. This line forced a move for the city's passenger traffic to a new station at Cahill, placing it one mile from downtown (whereas it had previously been a four-block distance). Passenger service along the Ocean View Branch ended after November 1928.

SP's Peninsula Commute experienced record ridership during World War II. During the war, 26 trains ran between San Jose and San Francisco per day, with headways as low as 5 minutes (traveling north) in the mornings and 3 minutes (traveling south) in the evenings. After the war, a May 1946 railroad strike displaced approximately 10,000 train passengers onto highways, causing "historic" traffic jams along the Bayshore Highway, with commute times for some automobile drivers to balloon from 30 minutes to 75 minutes going from Burlingame to San Francisco, a distance of approximately 19 miles (31 km). In 1954, surveys comparing traffic on Bayshore Highway with train traffic concluded that just over half of all commuters to San Francisco passing through Brisbane were taking the train, and that eight more lanes would need to be added to the freeway to accommodate traffic if rail service were to stop suddenly.

However, in the period after the war, Peninsula roads were improved; the four-lane undivided Bayshore Highway (completed in 1925) was rebuilt into a six-lane divided freeway between 1949 and 1962, and Interstate 280 was completed in the 1970s. Train ridership declined with the rise of automobile use, falling from a peak of 9.2 million annual boardings in 1954 (approximately 16,000 weekday riders) to 4.4 million in 1977 (approximately 7,000 weekday riders). Service to Los Gatos ended in 1959; the railroad noted the ease of reaching Vasona, the new end of the line, via automobile. The Mayfield Branch saw its last service in 1964, with its right of way reused in construction of the Foothill Expressway.