It is a primary transfer point for several local and regional bus operators, and a commuter rail station on the Sonoma–Marin Area Rail Transit (SMART) system.

The original San Rafael railway depot that served the Northwestern Pacific Railroad was located at what is now a cafe north of the station.

As rail use fell into decline, passenger service ended after November 10, 1958.

[8] San Rafael Transit Center has two side platforms serving the two tracks of the SMART mainline.

[9] San Rafael is the primary transfer point for Marin Transit, which operates local service plus two interurban routes.