The Ninja Warriors is a beat 'em up game that plays in a side-scrolling manner similar to the 1987 arcade version. The player can choose to play as one of three androids with ninja skills: the slow but powerful "Ninja" armed with a nunchaku, the quick but weak "Kamaitachi" with sickles on his arms, or the balanced "Kunoichi" who wields knives and swords. Per the story, the androids were built by a rebel faction to help them overthrow the tyrant Banglar ruling over their nation. After a sudden attack by Banglar's forces, the rebels had to release the androids to fight, untested.

The player can move along a single plane, with the stages typically going in a linear direction and ending with a boss. Each character has a different set of moves which include speed dashes, jumps, grabs, blocks, and a variety of attack moves. There is a power meter that increases slowly with time that, when full, lets the player trigger a powerful attack that damages all enemies on the screen. The meter drains completely if the player is knocked to the ground. Some items, such as motorcycles and large safes, can be picked up and tossed at enemies. The environments occasionally introduce hazards that can hurt the player as well as enemies, such as mine fields or armed helicopters. The Ninja Warriors has eight stages and unlimited continues. The player character can be changed when using a continue.