[3] The first station was approximately half a mile northwest of the current site; it was relocated two years later after residents complained the location was inconvenient and William Paul, a storekeeper and benefactor of the town, donated land on what was then Lincoln Street.

The station built in 1869 was replaced in 1955, and again in 1983 in conjunction with the development of the nearby Palo Alto Central condominium complex.

Until 2008, the station had a central boarding platform and could only accommodate one train at a time, necessitating a hold-out rule.

That year the station was reconfigured to have two outside platforms and a pedestrian underpass replaced the former at-grade crossing, eliminating the need for the hold-out rule.

[5] New shelters for passengers needing assistance are located at the northern end of the platforms, next to the manual wheelchair lifts.