In the 21st century, the evil Emperor Garuda has taken over the city of New York, killing many of its inhabitants. You play as either Hayate or Kaede, two ninjas who are attempting to free the city from Garuda's control.

Shadow of the Ninja is a typical side-scrolling action game, consisting of running, slashing and jumping through 5 levels, each with 4 sub-stages with numerous and varied foes, and a boss enemy at their end.

Kaede and Hayate can not only jump; as ninjas, they can hang from platforms and make swift saltomortals between floors. Sometimes, canisters containing powerups can be found. Typical powerups extend range of the default sword, or they may be additional weapons such as throwing stars and a ninja weapon that looks like a big grappling hook on a string.

As with a great many NES action games, but unlike the very similar (and tangentially related) Ninja Gaiden series, the game allows two players to play cooperatively.