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.

Gbagbo, 65, had been charged with undermining state security.
Her husband, former Ivorian President Laurent Gbagbo, is awaiting trial at the International Criminal Court (ICC).
More than 3,000 people died in the violence that followed the presidential poll after the ex-leader refused to accept defeat to Alassane Ouattara.
She and her husband were arrested in 2011 after troops stormed a bunker where the pair had taken refuge in the main city, Abidjan.
And it was in the same city where Gbagbo - once called the "Iron Lady" and known for her fiery speeches - faced trial. She was also accused of disturbing public order and organising armed gangs.
She denied witness accounts that accused her of personally distributing arms to the death squads that operated in Abidjan during the five-month conflict.
The court unanimously sentenced her to 20 years, which is the sentence for undermining state security.
The prosecution had only asked for 10 years - but this had only been for the charge of disturbing public order.
The BBC's Ali Bamba in Abidjan says the verdict was delivered in the early hours of Tuesday morning after eight hours of deliberation by the jury.
The former first lady remained calm, as she had been throughout the trial, almost as if she knew what was coming, he says.
Her daughter from a previous marriage, Marie Antoinette Singleton, told the BBC's Newsday programme that the sentence was unfair and a sign of "political justice".
"Why would you want to double it? It's not about justice; it's about getting rid of political adversaries.
"If we say that something wrong happened, it happened on both sides. Nobody looked into bringing all responsible parties to trial," she said.
Simone Gbagbo's lawyer said they would appeal.
"I was expecting Simone to be acquitted," Rodrigue Dadje told the BBC French service.
"There is no proof of her involvement at a personal levelâ€¦ I am ashamed for the Ivorian justice system."
The former first lady was on trial with 82 other supporters of her husband  - 15 of whom were acquitted.
Two former military allies also received 20-year jail terms: Gen Bruno Dogbo Ble, once head of the Republic Guard, and the ex-navy chief Adm Vagba Faussignaux.
The other accused got lesser sentences.
Before her sentencing, Simone Gbagbo had said that she forgave the prosecution, despite the humiliation she had suffered during the trial.
"I forgive because, if we don't forgive, this country will burn," she said.
Both sides were accused of atrocities in the conflict that followed the 2010 poll.
But our correspondent says despite a promise from President Alassane Ouattara that both sides would face justice, no-one in the president's camp has been charged.
Laurent Gbagbo, is facing four charges at the ICC in The Hague, including murder, rape and persecution.
The ICC had issued an arrest warrant for Simone Gbagbo too, but this was dismissed by the Ivorian government.
A motorist crashed through a fence and onto a train track, causing several hours of delays for passengers.
[NEXT_CONCEPT]
Ivory Coast's former first lady, Simone Gbagbo, has been sentenced to 20 years in jail for her role in the violence that followed the 2010 elections.