The Santa Clara passenger depot, the oldest operating railroad depot in California, was constructed by the San Francisco & San Jose Railroad Company in 1863. The 24'x50' board and batten depot was one of the two "way stations" built between San Francisco and San Jose. Plans for a railroad linking San Francisco and San Jose began as early as 1851. Though this scheme ultimately failed, the incorporation of the San Francisco and San Jose Railroad in 1859 met with success. Most of the financing for the project came from county government in San Francisco, San Mateo and Santa Clara counties, with the University of Santa Clara and local industry also playing a significant role in both stock acquisition and choice of placement of the depot in Santa Clara. The first passenger service to San Francisco started in January 1864. The Southern Pacific Railroad acquired the San Francisco & San Jose Railroad in 1868. The depot, originally erected on the east side of the railroad tracks, was moved to its present location in 1877 and attached to the existing 32'x50' freight house constructed several years earlier. Also, because of the large volume of agricultural freight shipped from the depot, the freight house was increased in size at that time to its present dimensions of 32'x160'.
On November 1, 1877, the San Jose Mercury reported the facility nearing completion. 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. Rail service provided the fast, direct link to San Francisco and, in the later 1870s, to Southern California. Typical of these efforts were those of James A. Dawson, who pioneered the area's fruit-canning industry in 1871. 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. Caltrans acquired the depot from Southern Pacific in 1980. In cooperation with California Department of Transportation, the South Bay Historical Railroad Society, a nonprofit group founded in 1985, began renovation work in 1986 on the depot, by then badly in need of repair. A group of dedicated volunteers spent over 25,000 hours hauling away debris, replacing support timbers, siding, exterior decking and interior flooring, scraping peeling paint, painting and many other repairs. With the major renovation now complete, this 139-year-old building hosts a railroad library and museum while still serving its original function as a passenger depot.