Caltrain spokeswoman Christine Dunn said the man was struck by southbound train No. 142 at about 11:45 a.m. just north of the Hayward Park station.
The train that hit the man had departed from San Francisco at 11:07 a.m. and was making all local stops, she said.
There were 400 passengers on the train, and no passengers or crew members were injured, according to Dunn. The northbound track reopened at 12:20 p.m., and service began getting back to normal.
The man's death marked the eighth fatality on Caltrain right-of-way this year, Dunn said. Last year, 16 people died on Caltrain tracks.
The circumstances of today's death remain under investigation, and the man's name has not been released.