BART police say the man - whose name has not been released - may have been caught in a crossfire during a shooting outside the Bayfair station around 12:20 p.m. Saturday.
The shooting also left a woman with wounds that were not considered to be life threatening.
One person was arrested after the shooting. The suspect's name or age has not been released.
Officials have not said what may have sparked the shooting, but detectives were reviewing surveillance video and following up on leads.