A northbound Amtrak Capitol Corridor train struck the man on Caltrain tracks near Virginia Street at about 7:45 a.m., spokeswoman Christine Dunn said.
No passengers were aboard the train, which Dunn said was being moved to the San Jose Diridon station.
The man was transported to a hospital for treatment. Dunn did not yet have information on his condition.
The incident delayed four Caltrains - northbound Nos. 227 and 233 and southbound Nos. 208 and 210, Dunn said.
Bus shuttles took passengers between the Tamien and San Jose Diridon stations during the brief disruption.
The tracks reopened and service began normally as of about 8:40 a.m., Dunn said.
