Gameplay consists entirely of Microgames. The player clears stages of microgames of a certain category, programmed by one of Wario's friends. Each microgame lasts only a few seconds. During this short time limit, the player must both work out what he is supposed to do and do it, aided by a word or short sentence that appears on top of the game as the time begins. Control is very simple - the only buttons used are the directional pad and A button. Failing to complete the microgame means the loss of a life, and losing four lives requires the player to start the level over. After clearing a set number of microgames (either 10, 15, 20, or 25) the player must win a longer "boss" microgame which is generally more challenging in order to clear the level.

After clearing levels, bonus games like ropejumping or Dr. Wario (a remake of Dr. Mario) become available to the player. Some of these games are two-player and require the use of the "L" and "R" buttons. Cleared stages can be replayed indefinitely, with each level of play faster and harder than the previous. Individual microgames can be accessed as well for the player to practice, provided that they have been played at least once in the normal mode. After all the levels are cleared, different modes of play are available, like Thrilling, in which the player only has one life, or Easy, where the game speed never increases.