The crash was reported at 10:36 a.m. at the railroad crossing near Lewis and Upland roads.
Authorities say an Amtrak Surfliner 765 hit a vehicle that was apparently stopped on the tracks.
Investigators say the engineer saw the car stopped on the tracks and applied the brakes but was unable to stop in time.
The driver, who was the only person in the vehicle, was airlifted to a local hospital and pronounced dead there.
She was identified as a 63-year-old woman believed to be transient.
The collision remains under investigation.
Nobody on the train was injured but the line schedule was delayed.