Featuring gameplay similar to the Super Famicom title Ganbare Goemon 3: Shishijūrokubē no Karakuri Manji Gatame, the game presents a story where Yae has been kidnapped by the Black Ship Gang.

Mystical Ninja Starring Goemon featured three characters—Goemon, Sasuke, and Ebisumaru—who can walk, jump, attack, and throw weapons throughout five stages of play.

[3] The magazine's editors enjoyed the expansive world, but criticized the quality of certain graphical elements, noting that certain hazards and features were "hard to distinguish".

The controls received average marks, with Nintendo Power's reviewers decrying the difficulty of dodging due to the high speed of enemy projectiles and movement problems with boss battles.

Writers compared the game to The Legend of Zelda series in design, but criticized the automatic regeneration of enemies in each stage—a tenet which made retracing one's steps tedious.