The game has eight levels, each of them broken into two sections, and with bosses along the way. The control scheme allows you to dash, attack, jump and throw shurikens. A lock-on feature is also provided. It should be noted that the game also has a few hidden features such as holding attack during lock-on to do a charge attack, double jumping and throwing shuriken to do a shuriken burst, and a stun kick by press down and attack while locking on.

The main objectives of the levels is to kill. No item fetching is required, however the ninjutsu scrolls come in handy, and some levels require Hotsuma to break stone pillars to continue. Shinobi also contains combo features. One of these features is called a "tate" kill, whereby if enemies are killed in a chain, a cutscene will play killing all enemies at once and dropping more Yin for your blade. The other feature is that as Hotsuma kills with his cursed blade "Akujiki", the sword will change different colors indicating different damage multipliers.