Charlie Ninja is a 2D side-scrolling platform game that puts players in the shoes of a ninja that throws throwing stars and other typical eastern weapons at enemies. The player can also cloak himself so that he becomes invisible for enemies and can evade attacks. Melee attacks are also possible.

Each of the stages has a different theme and a boss with a bounty at the end. The settings for the stage are the wild west, army, dilapidated industrial zone, football stadium and a mad scientists lab. Enemies attack the player directly or shoot projectiles at them. Weapon power-ups can be collected from defeated enemies and sometimes fire walls have to be circumvented. The game can be played solo or with a friend.