The gameplay is straightforward: on the DS, use the stylus to tap at moles; on the GameBoy Advance, navigate a marker around the screen using the directional pad. The game features three modes: arcade mode, where you must reach points before time runs out; puzzle mode, which includes recreating shapes and solving puzzles like Tic Tac Toe and Peg Puzzle; and quick play mode, allowing you to choose levels and difficulty.
As you progress through the game, you'll encounter various moles with different behaviors, such as ninja and bazooka moles that attack your score. Power-ups like multipliers, clocks, and bombs will also aid or hinder your progress. With seven worlds to explore, each with its own graphical theme, Whac-A-Mole offers a fun and challenging experience.