The collision happened on the VC Line 121 to Moorpark just after 7 p.m. in the area of Los Angeles Avenue and Tapo Street.
The car sustained "moderate damage" according to the Ventura County Fire Department. The driver was treated for injuries at the scene and then transported to a local hospital.
No train passengers were injured.
The train remained stopped on the tracks and Metrolink service in the area is expected to be delayed.
The circumstances that led to the crash were under investigation.