Super Ninja-kun tells another story in Ninja-kun series. Ninja’s girlfriend was kidnapped by a demon and it’s up to the player to get her back.
As in previous games, Ninja can shoot shurikens, climb walls and collect various weapons like bombs and boomerangs. New to the series is the ability to run and a longer health bar represented by hearts (a single shuriken doesn't kill the player anymore). Hearts can be collected to add more health. When the ninja dies, he is resurrected on the spot. Ninja also collects souls of slain enemies to fill his soul gauge. When the gauge is filled, Ninja can unleash one of his super powers.
The game contains a total of 9 stages with a boss battle at the end of each one.
The game also features a simultaneous two-player mode, the second player being a palette swap of Ninja-kun.