In late 1863, the Santa Clara Train Depot was constructed by the San Francisco and San Jose Railroad Company as one of two “way stations” built between San Francisco and San Jose, the original 24 foot by 50 foot passenger portion of the depot was built on the east side of the tracks. The first regular through passenger service to San Francisco started on January 17, 1864. When the transcontinental railroad was completed in 1869, the first shipment of fresh fruit, a carload of pears from the Santa Clara depot, was sent from California to the eastern states in October, 1869.
In 1985, the South Bay Historical Railroad Society was established. The historical society manages the Edward Peterman Railroad Museum within the depot, which is next to an active Cal Tran line.