Mini Ninjas is a linear third-person action-adventure game. It features six playable Mini Ninja characters, each with their own unique abilities, weapons and skills. Players can collect special weapons, including caltrops, shuriken, different bombs and fishing rods, and a multi-functional ninja hat, as well as a variety of potions and food items. The main protagonist, Hiro, can cast spells, including fireball and lighting attacks, camouflage, and time manipulation. Hiro can also possess spirits, such as animals, for a short period of time. Spells are cast using Ki, which is dropped by enemies and can be replenished with potions.
The enemies in Mini Ninjas are animals enchanted by the main antagonist, turning them into samurai warriors. When defeated, the curse is broken and the enemies return to their previous animal form, and can assist the player. For example, brown bears can attack with their claws, warthogs charge at enemies, and panda bears can slam into the ground. All animals have a keen sense of smell for spotting ingredients and collectibles in places that are easily overlooked. Other enemies in the game include ghosts, which approach the player and attempt to drain their life force.
Throughout their journey, players can collect coins and ingredients, such as mushrooms, flowers, and ginseng roots. They can exchange these coins for weapons and recipes from the Tengu, crow-like humanoids who also give quests and advice. Fruits found on trees or bushes can be harvested by shaking the bushes or the trunk of trees, which will restore their health. Other foods like sushi do the same thing.
Scattered throughout the world are ancient shrines, each containing a scroll that grants Hiro a new spell. There are also 100 Jizo statues hidden throughout the game, which can be collected for special achievements or trophies.