Earthworm Jim: Special Edition features all the content from the Mega Drive version of Earthworm Jim, but includes an extra level, "Big Bruty". Other levels have been expanded, and there are now three different (fully voiced) endings depending on the difficulty chosen. Other additions include a new homing missile weapon, a password system, new cheat codes and some new animations in the introduction and endings of the game.
Being a Mega-CD game, Special Edition features an enhanced CD audio soundtrack, and features more voice clips (all of which are clearer then their Mega Drive counterparts). On the other hand, CD loading times are introduced between stages.