Both New Jersey Transit and Amtrak trains were impacted for several hours.
NJ Transit says rail service into and out of Penn Station New York is now operating on or close to schedule.
Amtrak says at around 2 p.m., one set of wheels on Train 133 derailed while leaving Penn Station.
"Part of the train was still at the platform, allowing customers could safely and quickly depart the train. Customers are accommodated on other trains departing New York," Amtrak said in a statement.
The Office of Emergency Management said FDNY operations have concluded, and the impacted train was brought back to the station. They say Amtrak will then move the train out of the station to restore service.
Customers impacted by the delays should expect delays of at least 20 minutes.
Amtrak said it will waive additional charges for customers who need to change their reservation during the modified schedule by calling the reservation center at 1-800-USA-RAIL.
NJ Transit rail tickets and passes will no longer be cross honored by PATH at Newark Penn Station, Hoboken Terminal and 33rd ST-NY.
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