The original 16th Street depot was a smaller wood structure, built when the tracks were on the shoreline of San Francisco Bay.

[2] The original depot was replaced by a Beaux-Arts building designed by architect Jarvis Hunt which opened for service on August 3, 1912.

It was a companion (or "city station") for Oakland Pier, two miles away, where passengers could board ferries to San Francisco.

The station was severely damaged in the 1989 Loma Prieta earthquake, but continued serving trains at an adjacent building.

[10] Emeryville largely replaced 16th Street station as the connection point for Amtrak Thruway across the bay in San Francisco (for passengers heading northbound towards Seattle or eastbound towards Chicago, or passengers arriving from the north and east), as Emeryville is closer to the San Francisco–Oakland Bay Bridge than Oakland–Jack London Square.

The station was purchased in 2005 by BUILD, an affiliate of BRIDGE Housing, and is being restored as part of a local redevelopment project.