Mini Ninjas is set in a world where an ancient warlord has returned with a demonic army, transforming innocent animals into fearsome warriors. The player takes control of Hiro, a young ninja, and his friend Futo as they journey through different worlds to restore balance to nature. The game features a third-person perspective with a relative amount of freedom to explore the environment.
Gameplay involves following the steps of other warriors and eventually freeing them to make them playable. Players can switch between any character at any given moment, each with their unique abilities. Hiro has Kuji spells that include fireballs, whirlwinds, and spirit form, while Futo wields a large hammer and is useful against larger enemies. As the player progresses through the game, four more characters become available, including Suzume, Shun, Tora, and Kunoichi.
The gameplay features basic attacks, defence breakers, and acrobatic moves such as wall jumping and running along walls. Characters also have a sneak mode to hide in the environment and cause more damage when attacking or avoiding confrontations. Health is restored by gathering fruit, and collectible items can be used to create potions, bombs, and power-ups. As characters level up, they gain better abilities and focus attacks.