Emergency services were called to the line near Stanford-le-Hope, Essex, at about 21:30 GMT on Monday.
A tow truck had to be called to remove the car, which was stuck on the track. No one was trapped or badly hurt.
The 18-year-old driver was arrested at the scene on suspicion of theft of a motor vehicle, driving without insurance and careless driving.
Train operator c2c apologised for delays to passengers.
It said services were disrupted for about three hours while the car was removed and Network Rail engineers examined the track and repaired the fence.
A motorist crashed through a fence and onto a train track, causing several hours of delays for passengers.