Pixel Shinobi is a game in the genre of stealth and platforming with elements of RPG, in which the player plays as the Shinobi (Ninja). The player can gain experience when killing enemies and eventually be able to unlock more advanced ninjutsu.Going through the levels the player will collect the various ingredients in which he can craft weapons: shurikens, poisons, elixirs, grenades, mines, as well as the main weapon the Ninjato and Kusarigama. At the end of each level the player gains experience for the past level completed, the game utilizes a stealth mechanic in which hide and seek can be your best weapon of defense and offense. Being able to hide in the shadows and deliver crucial and critical blows to an enemy can also give you experience in the end.

After each level the player will be returned back to their home village in which they are able to purchase weapons, items and more advanced ninjutsu in the game.