Caltrain officials reported on Twitter at 2:32 p.m. about the collision involving northbound Train No. 151 heading toward San Francisco.
The collision occurred near Howard Avenue, just south of the agency's Burlingame station, involving a man trespassing on the tracks.
Bus shuttles took passengers around the scene until the southbound tracks reopened, allowing trains to single-track through the area as of about 3:15 p.m. The bus bridge was cancelled at 3:26 p.m. Delays of up to 31 minutes have been reported.
Tuesday's death was the 12th fatality involving Caltrain in 2016.