It is the planned terminus for the Silicon Valley BART extension into Santa Clara County on the future Green and Orange Lines.

The depot, originally on the east side of the tracks, was moved to its present location in 1877 and attached to the existing 32-by-50-foot (9.8 m × 15.2 m) freight house constructed several years earlier.

Following construction of the railroad, farming and fruit-related industries developed in the Santa Clara area, with the depot serving as a focal point for shipping.

By the turn of the century, the Pratt-Low Preserving Company, the largest fruit packing plant in central California, was located just south of the depot.

In cooperation with the South Bay Historical Railroad Society, a nonprofit group founded the same year, they began renovation work in 1986 on the depot, by then badly in need of repair.

ACE service to Santa Clara resumed on May 14, 2012; Amtrak Capitol Corridor trains began stopping at the station on May 21.

Santa Clara was chosen as the terminal because of the access to the San Jose International Airport as well as the proposed BART maintenance facility located in the vicinity of the station at the former Union Pacific rail yard.