The gameplay of Boogerman operates as a simple side-scroller, with burp/fart ammunition, as well as booger ammunition. There are 20+ different levels, as well as a final boss level. Each level consists of a slight puzzle to finish to the end, and to accomplish this it is necessary to defeat foes, unique to each level. Following this boss battle is a "sandbox" playable credit scrolling, as the player is able to "fly-fart" with unlimited fuel (something the player is not able to do during normal gameplay).
Throughout the game, Boogerman's health is represented by his cape which will change from red to yellow whenever he takes damage from enemy attacks, and if he is hit while his cape is yellow, he loses a life. The player can gather capes to restore Boogerman's health. Also scattered through the levels are huts that will activate checkpoints if touched.