The boy was riding between two cars of a southbound L train when he attempted to jump to the New Lots Avenue station platform in Brownsville around 10:30 p.m. Wednesday.
He missed and landed on the tracks.
The teen was rushed to Brookdale Hospital where he was pronounced dead.
The teen's death comes just days after an apparent subway surfer was killed hanging onto the side of a train Greenwich Village.
Quentin Watkins, 31, was hanging onto the side of a Brooklyn-bound F train when he hit something just as the train entered the tunnel at the West Fourth Street station at about 3 p.m. Saturday.