The HBO documentary Leaving Neverland prompted executive producer James L. Brooks, creator Matt Groening and showrunner Al Jean to make the decision, which upset fans of the show.
The Simpsons episode 'Stark Raving Dad' introduced Leon Kompowsky, a character who believes he is Michael Jackson, and voiced by the US singer.
Executive producer James L. Brooks said that pulling the episode felt like "clearly the only choice to make."
"The guys I work with — where we spend our lives arguing over jokes — were of one mind on this," Brooks told The Wall Street Journal.
Leaving Neverland, produced by HBO, shows James "Jimmy" Safechuck and Wade Robson claiming they had suffered sexual abuse at the pop star's hands while spending time with Michael Jackson as children.
The film caused an outcry among Michael Jackson fans and critics alike, and has recently prompted the star's daughter Paris Jackson to speak out on Twitter.
READ MORE: Michael Jackson's Daughter Speaks Up Amid Frenzy Over Leaving Neverland Doc