Bay Fair station has a single elevated island platform serving the line's two tracks.

A pedestrian tunnel under the Union Pacific Railroad Oakland Subdivision tracks connects the fare lobby to parking areas south of the station.

An AC Transit bus transfer area and additional parking are located on the north side of the station.

Elevators at most of the initial stations, including Bay Fair, were completed in the months following the opening.

[5] Thirteen BART stations, including Bay Fair, did not originally have faregates for passengers using the elevator.