The metre-long shark's body was found lying on the floor of a carriage by passengers catching a late-night train to Queens overnight.
Believed to be a Mustelus canis shark, or a smooth dogfish, it is not yet known how it came to be there.
But photos uploaded by witnesses have sent social media sites into a frenzy as they are shared all over the globe.
Most New York Metro commuters have been bemused by the discovery, with some making references to comic action films Snakes on a Plane and Sharknado.
One photo shared on Twitter shows the shark having been placed with a cigarette and metro card.
Some Twitter users have branded the shark as a marketing ploy on behalf of the Discovery Channel's "Shark Week".
Others were simply horrifed at the death of an innocent creature, believing it the sign of unjustifiable cruelty.
Citing a spokesman for the Metropolitan Transportation Authority, The Wall Street Journal reports that the train's conductor only became aware of the shark once the train arrived at Queensboro Plaza.
The conductor then isolated the car before completing the journey, where upon he reported the shark was dead, placed it in a garbage bag and disposed of it in the trash.
It is prohibited to take sharks and other animals on board the New York City subway.
