Northbound train No. 143 hit the person at Peninsula Avenue in Burlingame at 12:23 p.m.
The train left San Jose at 11:10 a.m. and was making all local stops. There were about 900 passengers on board, and they will now be transferred to another train, Caltrain spokeswoman Christine Dunn said.
Delays of up to 90 minutes are expected, Dunn said.
As a result of a fatality in Burlingame, Caltrain is not operating on either the northbound or southbound tracks between San Mateo and Millbrae. SamTrans will set up a bus bridge between San Mateo and Millbrae.
ABC7 contributed to this report