Northbound train No. 103, heading from San Jose to San Francisco, struck the person at 6:32 a.m. between Tunnels 2 and 3 near the 22nd Street station, according to the transit agency.
No injuries were reported among the roughly 75 people aboard the train at the time, and the person struck was trespassing on the tracks, Caltrain officials said.
The collision initially stopped trains from going through the area in either direction. The southbound tracks reopened shortly before 8 a.m. and the northbound tracks reopened by 8:22 a.m., according to Caltrain.
Authorities are working to determine whether the death was intentional or accidental. The name of the person killed has not been released.
The death is the 12th on the Caltrain right-of-way in 2019.