Montreal, Maine & Atlantic Ltd (MMA) filed for bankruptcy in the United States and Canada as it faces mounting pressure from authorities to pay for the disaster clean-up.
In court documents filed with the US Bankruptcy Court in Maine, the company said it was making the application to preserve the value of its assets for a potential sale.
The Quebec crash on 6 July was the worst of its kind in North America in two decades.
The driverless MMA train careened into the small town of Lac-Megantic, where it derailed, causing massive explosions and a wall of fire that obliterated the town centre and killed those in its path.
An estimated 5.6 million litres of oil were spilled.
As clean-up costs and lawsuits piled up, the company had hinted that it might opt for bankruptcy.
The Quebec government has ordered MMA as well as World Fuel Services, the company whose unit sold the crude oil the train carried, to pay for cleaning up the oil that spilled in the crash.
The municipality of Lac-Megantic has so far paid C$7.8m (€5.7m) to companies doing the clean-up and is demanding the railway pay it back.
MMA said total monthly revenues of its Canadian and US units had dwindled to about $1m since the derailment, given the closure of its main line between Quebec and Maine.
In a statement, MMA Chairman Ed Burkhardt said: “It has become apparent that the obligations of both companies now exceed the value of their assets, including prospective insurance recoveries, as a direct result of the tragic derailment at Lac-Megantic, Quebec, on July 6.”
He said the company wished to work with authorities “in the continuing environmental remediation and clean-up as long as is necessary, and will do everything within its capacity to achieve completion of such goal”.
The company said it had assets of between $50m and $100m and liabilities of up to $10m.
The court documents said the loss of much of the company’s freight business occurred because Canadian authorities are not letting its trains run between Maine and Quebec.
MMA said it will continue to provide essential rail services in Quebec, Maine and Vermont and services to Lac-Megantic will be restored when authorities allow it.
However, Mr Burkhardt made clear earlier this week MMA would no longer transport oil.