First responders told KTVU it happened about 1 p.m. Saturday between the Bayshore and 22nd Street stations, south of Tunnel 2 and just east of Interstate 280 north.
There were more than 270 people on board the train at the time.
It's unclear why the person was on or near the tracks.
No other injuries were reported.
The cause of death is under investigation.
The medical examiner has not yet released the victim's identity.