The unlikely passenger, about 1.2m (4ft) long, was found under a row of seats on a Queens-bound train.
The conductor asked passengers to leave the carriage and the train continued to the end of the line, where a supervisor disposed of the shark.
Pigeons and even an opossum have made their way on to the trains before, but never a shark, transit officials said.
However, where it came from remains a mystery.
Isvett Verde, of Brooklyn, New York, who took a photo of the shark, said she noticed that the empty carriage of the N train "smelled extremely fishy" when she boarded at 8th Street.
"It's hard to be surprised as there are always crazy things happening in this city, but even that was a bit much," she told the BBC.
Other pictures of the exotic discovery have also gone viral, including one of the shark with a cigarette in its mouth next to a fare card and a can of energy drink.
What did you expect? It's "Shark Week" on Science Channel...
;-)