Egg Mania is a puzzle game in which the player controls an egg shaped character against either a computer opponent or another player via the link cable. The object of the main modes is to build a tower tall enough to reach a balloon at the top of the play field before the opponent does. If the player tries to take a short cut and not build complete floors, the structure will start crumbling and the water will come up faster. There are plenty of obstacles, both from the game and from competing opponents. Falling meteors can knock the player down into the water, while bombs thrown by the opponent will destroy parts of the player's structure. The main modes include Over Easy and Hard Boiled, the difference being that in the latter a different difficulty can be chosen.

There are four extra modes: Survival, Solo, Time Trial and Bomb. In Survival the player must survive as many rounds as possible, while the goal in Solo is to increase the overall score by completing rows and performing combos; Time Trial challenges the player to continually beat his or her own best time; finally, in Bomb, whoever destroys the opponent's tower first wins.

Compared to the GBA version, the console versions have improved graphics and sound, cutscenes at the beginning of each level, a play area that is wider by one block, two additional modes (8-player Tournament and Custom, where the rules can be customized by activating different options), but lacks the Time Trial mode. Otherwise they are completely identical, both in gameplay and level design.