The sedan's driver failed to navigate a turn and ended up on railroad tracks near Palm Avenue and California Street shortly after 6 a.m., sheriff's Deputy Jeffrey Houser said.
Houser said the driver hopped out of the car and tried to signal the northbound train's operators as it approached at about 35 miles per hour, with horn blaring.
The engineer activated the emergency brakes, slowing the train, but was unable to avoid the crash. Authorities said the driver was not injured, but the car sustained major damage.
Authorities closed the tracks for about an hour, Houser said. A couple of Amtrak routes were canceled, but officials with the North County Transit District said ticketed Amtrak passengers would be allowed to take Coaster trains instead.