By Agence France-Presse
Inbound and outbound services from the station were suspended.
The cause of the derailment was not immediately given.
The train was run by New Jersey Transit, which links towns in that state across the Hudson River to the US financial capital.
There have been several mishaps in recent months at Penn Station.
This latest incident comes as crews prepare to undertake major rail line work from July 10 at Penn Station, expected to cause further delays for commuters for six weeks.