One dark and stormy evening, the civic-minded Professor Stinkbaum was working in his lab where he was secretly building a machine that would save the world from pollution by transporting it to a place he called Dimension X-Crement. That same evening, eccentric millionaire Snotty Ragsdale paid a visit to the lab to investigate this project and to find out how such a thing was possible. He wasn't too sure about the machine's purpose. When the machine was activated, a cloud of pepper was inhaled through the nose by Ragsdale, causing him to let out a mighty sneeze. The power of said sneeze broke the machine. As a result of it breaking, a portal opens from it. Just then, a mysterious giant arm pops out of the portal and steals the machine's main power source. In response to this danger, Snotty rushes into the men's room to change into his alter ego, the mighty Boogerman! After doing so, he jumped into the portal to pursue the arm to learn the reason for the theft it had committed.

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).