Samuel Rausenbush, a 20-year-old Piedmont resident, was considered trespassing on the tracks along the Capitol Corridor when he was hit by a westbound train at 6:02 a.m.
More than 50 passengers were on board when the accident occurred, but no other injuries were reported.
Trains were operating on a single track while crews were on scene conducting an investigation.
The passengers got off the train, which originated in Sacramento, and switched to another train bound for San Jose.
The nearest designated crossing area is at Central Avenue in Richmond, about one-quarter mile south of where Rausenbush was hit.