The man, whose identity has not been released, was pronounced dead at the scene, an FDNY spokesman said.
He was struck about 5:40 a.m. by a northbound A train near the Fort Washington Avenue-West 175th Street subway station, an MTA spokesman said. About 100 people were evacuated from the train after the incident.
It was not immediately clear how the man ended up on the tracks. A spokeswoman for the NYPD said there was no criminality involved.
A train service was suspended in both directions between the 168th Street and Inwood-207th Street stations, the MTA reported. C trains were also experiencing delays due to the collision and ensuing police investigation.
For updates on service changes, check the MTA's website.