The game features four main levels, which can be entered in any order. The player must reach the end of each level and beat the boss to obtain a piece of movie memorabilia. After clearing all four levels, players travel to the final level where they must fight Pinky and the Brain. Players control Yakko, Wakko, and Dot, switching control between them to use their respective powers accordingly. Yakko uses a paddleball to stun enemies, and is also able to push and pull objects such as crates. Wakko uses a mallet which can be used to hit switches, break certain objects and light fuses. Dot is able to blow kisses which, when used on certain characters, triggers certain actions needed to progress.

The Warner Brothers and Sister have health indicators and a number of lives. The lives can be increased by obtaining either 100 stars, or obtaining a small golden form of their faces. Their health is indicated by their faces on the top left of the screen. When they smile, they are healthy, but when they are looking either tired, unhappy, or weak, then they should find health soon (which is found in the forms of several forms of ice cream or sweets or other kinds of food). The levels are timed.

This version was ported to the Game Boy by Factor 5, but due to space constraints, only three levels are present in this version and certain parts of the three levels are absent. Both the Science Fiction/Space Opera – Space Wars (Space Trucking) and nearly all of the final Action Movie - Once There Was A Man Named Oscar levels are absent from this version. On easy mode, the Game Boy version ends early, on the first three levels. On normal and hard modes, the Game Boy version continues after the player completes the first three levels, goes to Once There Was A Man Named Oscar, and battles Pinky and the Brain.