It happened around 6:30 a.m.
Investigators say the man was trespassing on the tracks.
About 300 people were aboard the train and none were hurt.
The fatality is the sixth on Caltrain's right-of-way in 2016, according to officials.
Incident at Oak Grove Ave crossing has been confirmed as a fatality. Bus bridge being established. #caltraindelays— Caltrain (@Caltrain) May 23, 2016