The northbound No. 101 train struck the victim at about 5:15 a.m. in the second incident in as many days, according to spokeswoman Christine Dunn.
The victim, who trespassed onto the tracks, has been transported to a local hospital. No other information on his condition was immediately available.
Passengers from the train involved in the incident have been transferred to the No. 103 train, which was behind the No. 101 train. The No. 103 train and southbound No. 102 train, are experiencing delays of about 20 minutes, Dunn said.
Caltrain also experienced delays Thursday morning when a train struck a vehicle on the tracks in San Jose.
The incident, which occurred at about 6:50 a.m. Thursday at a private crossing south of the Blossom Hill station, Dunn said.
The collision left the driver of the vehicle in critical condition as of Thursday afternoon, according to the traffic division of the San Mateo County Sheriff's Office.