In Dexter's Laboratory: Science Ain't Fair, Dee Dee has gotten into her brother's lab (again!), but this time she has really caused trouble. Not only did she destroy his science project, somehow her meddling has caused Dexter to be shrunk down to three inches tall! How on earth is he going to prepare for the science fair now? He can't let Mandark win! The boy genius must figure out how to return himself to normal size or all will be wrong with his world.
There are six arcade-style levels in Story mode which are played in order. Players take the role of Dexter and navigate him through his house while dodging forks, bubbles and other hazards until he reaches his lab. Dexter can use a bubble-like shield to protect him from some hazards. There he must finish his science fair project by constructing a robot. Besides building a robot, players will construct other contraptions, fly Dexter and his backpack helicopter, and gather bonus pieces. Four mini-games allow players to squash insects, shoot angry monkeys, and take secret photos of Mandark's lab.
The game features a Print Studio and Cartoon Maker for printing pictures, making cards and other projects as well as design custom cartoons. The Story Mode's auto-save function saves progress and allows replaying of completed levels at any time.