Jim's ability to spin his head like a helicopter has been replaced with the Snott parachute, which is performed by holding in the air. Instead, pressing while in the air will make Jim launch Snott in front of him to grab onto and swing from mucous-covered ceilings. He can still fire his gun by pressing and can still use his head as a whip with while on the ground, though he can no longer use his head whip in the air. Jim is controlled in much the same way as the original game, though with some new and changed abilities. As well as including standard platforming levels, there are also quiz questions, an isometric shoot 'em up level and various adaptions to the platforming formula, including marathon races and a stage where Jim must shoot his way through mounds of dirt.

Though very similar to the original game, Earthworm Jim 2 has more varied gameplay than its predecessor.

Jim, with help from Snott, has to follow their trail across the various summer homes of his enemies. However, Psy-Crow kidnaps the Princess and plans on marrying her at the Las Vegas system in order to take over the universe. Following on from the ending of the first game, Earthworm Jim had removed the cow (which he had unknowingly launched) from atop Princess Whats-Her-Name, reinflated the squashed lady, and won her heart.

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