A straphanger on the platform made the gruesome discovery at the north end of the track about 9 a.m. and immediately reported it to a station agent, an MTA spokesman said.
The transit system's rail control center halted an incoming train and told the crew on board to confirm there was a body on the tracks, the spokesman added.
The man, who was not immediately identified, suffered multiple trauma injuries and was pronounced dead at the scene, the FDNY said.
Investigators were looking into how the man ended up on the tracks or how he died. Transit officials initially said he had been hit by a train.
Investigators were interviewing train crews that had passed through the station before the man's body was discovered, a transit spokesman said.
Trains along the F line were temporarily disrupted Wednesday morning, but returned to normal service about noon, the MTA said.