At about 6:30 a.m., the man was hit in the pedestrian crossing at the north end of the San Bruno Caltrain Station, located at 481 Huntington Ave, spokeswoman Christine Dunn said.
He was hit by an express train that was coming through the station.
"The gates were down," Dunn said. "The lights and bells were all operating."
Dunn said Caltrain was still running on a single track as of 8:30 a.m.
Riders were experiencing delays of up to an hour at that time, and Dunn said it was unclear when service would be restored.