Palo Alto is the second-busiest Caltrain station after San Francisco, averaging 7,764 weekday boardings by a 2018 count.

The Caltrain station has two side platforms serving the two tracks of the Peninsula Subdivision and a nearby bus transfer plaza.

The station building was listed on the National Register of Historic Places as Palo Alto Southern Pacific Railroad Depot in 1996.

A temporary building for ticket sales, telegraphy, and baggage was constructed between the waiting room and a retrofitted former boxcar.

[3][6] Designed by SP architect John H. Christie, the building's aesthetics were inspired by the railroad's Daylight series of streamlined passenger trains.

[6][3] The station's design is typical of the Streamline Moderne movement; it has porthole windows, substantial use of glass blocks, and horizontal "speed lines" on the exterior.

[8][9] SP Peninsula Commute local service (renamed Caltrain in 1985) continued to stop at Palo Alto.

At Palo Alto, the northern underpass was modified to make it accessible, allowing the nearby pedestrian level crossing to be closed.

[15] Palo Alto is the second-busiest Caltrain station after San Francisco, averaging 7,764 weekday boardings by a 2018 count.

[2] A 2007 city report called for additional expansion and renovation of the station area in conjunction with the California High-Speed Rail project.

[16] In 2013, the Santa Clara Valley Transportation Authority proposed relocating the bus plaza onto both sides of University Avenue.

[17] Among the possibilities being considered for eliminating grade crossings in Palo Alto were a viaduct, a trench, and long tunnel under the downtown area.