The collision occurred around 7:40 a.m. involving northbound train No. 227, which runs from Gilroy to San Francisco, Caltrain spokeswoman Tasha Bartholomew said.
The woman, whose name hasn't been released, was trespassing on the tracks near the station at 3400 Monterey Highway, according to Bartholomew.
The train had 304 people on board, with no injuries reported.
All trains initially were stopped in the area, with bus shuttles taking riders past the scene. The shuttles were canceled and the train resumed service as of shortly after 9 a.m., Bartholomew said.
The San Mateo County Sheriff's Transit Police Bureau, which patrols the Caltrain right-of-way, will investigate the case. Bartholomew said it was too early to determine whether the woman's death was intentional or accidental.
The death was the sixth involving Caltrain in 2019.