It is the southern terminus of the South County Connector service, and is only served during weekday rush hours in the peak direction, with trains going toward San Jose in the morning and returning southbound in the evening.

Future plans call for extended Amtrak Capitol Corridor service, as well as California High-Speed Rail trains, to also stop at Gilroy.

The station was named to the National Register of Historic Places in 2019 as Gilroy Southern Pacific Railroad Depot.

[3] The original station was replaced with a two-story Italian Renaissance structure — framed with local redwood and covered in cement plaster — in 1918 by the Southern Pacific Railroad.

[3] In 1998, the city restored the station building as the centerpiece of the $2.8 million Gilroy Transit Center, which also included parking lots and a bus plaza.