Train 439 struck the car around 5:32 p.m., according to Caltrain spokeswoman Christine Dunn.
No one was inside the car when it was struck, however, and no one was injured, either in the car or on the train, Dunn said.
The accident briefly shut down service, but trains are now moving in both directions on the southbound tracks.
A tow truck is on the scene and preparing to tow away the car, and the affected train is being moved.
Because Caltrain operates only hourly service this time of day on Sunday, delays have been minimal, Dunn said.
Dunn said she didn't know how the car ended up on the tracks.