The northbound train hit the unoccupied car at 11:25 a.m. in the city's Potrero Hill neighborhood, Caltrain spokeswoman Christine Dunn said.
No one was injured in the collision, Dunn said. There were about 200 people on board the train at the time.
The train was stopped at the Bayshore station while a tow crew removed the car from the tracks, Dunn said. At about 12:15 p.m., the car was removed and Caltrain service started returning to normal.
There were no reports of delays to southbound Caltrain service.