The crash happened around 7:30 p.m. on the Rock Island line near 103rd and Vincennes in the city's Washington Heights neighborhood.
Metra said there were passengers on board at the time of the crash.
All passengers were transferred to another train.
There were no reports of injuries, and it appears no one was in the car that was on the tracks.
Photos from the scene show a black sedan with heavy damage to the rear.