There was originally going to be a Lemmings arcade port by Data East. The port got to the prototype stage before being cancelled. it was the first Lemmings game to include a "fast-forward" function, a feature that was later used in future ports and sequels.

The level editor for Lemmings used by DMA Design was based on Deluxe Paint's interface. The familiar interface meant they were able to create levels more easily, competing with one another to create the most difficult level designs that they could. Unfortunately this led to them having a large amount of hard levels, requiring them to go back and design new easier ones for the start of the game.

The impetus for Lemmings came from an animation created by Mike Dailly to prove he could draw recognizable human figures under an 8x8 pixel restriction (as coworker Scott Johnson was drawing them for another game under a 16x16 restriction). Gary Timmons added to the animation and also made the proto-Lemmings' walk cycle more fluid.

Lemmings was originally going to use a soundtrack of plagarised copyrighted music, something that was common in microcomputer games the decade prior, including pop songs and television theme songs. In the final game, these were swapped for public domain songs, though a sample of Don Messick as Scooby-Doo used for a cover of the Scooby-Doo & Scrappy-Doo theme song would be retained in the How Much is that Doggie in the Window? music track. The Mission: Impossible theme seems to have been chosen in reference to a fad on British television at the time of showing squirrels performing stunts to the song.

One of the music tracks in Lemmings, known officially as Lemming 1, is often referred to online as "Pachelbel's Canon in D Major". Despite this, the only resemblance between the classical piece and the Lemmings theme is their chord progression.