Super Ninja Boy features a password system to record progress.

The game was re-released on the Nintendo Switch Online service on January 24, 2025.

Battles take place in a beat'em up style and end after a specific number of enemies are killed (no matter how many are still remaining on screen).

Boss battles are fought in a turn-based RPG style, using the same items and skills as normally.

There are also some 2D platform areas, which play the same as the normal battles without depth (the player can only go right or left).