Ninja Master's follows the conventions of many previous 2D fighting games released for the Neo-Geo. The player must defeat their opponent in combat in a series of best-two-out-of-three matches. Characters can change between using the character's weapon or fight hand-to-hand during the middle of combat. Like the Art of Fighting series, Ninja Master's features a super meter.

Ninja Master's follows the conventions of many previous 2D fighting games released for the Neo-Geo. The player must defeat their opponent in combat in a series of best-two-out-of-three matches. Characters can change between using the character's weapon or fight hand-to-hand during the middle of combat. Like the Art of Fighting series, Ninja Master's features a super meter.