Two men, James Safechuck and Wade Robson, allege in a Channel 4 documentary that they were sexually abused by the King of Pop.
The Wall Street Journal says that producers of The Simpsons have decided to remove the episode, Stark Raving Dad, from streaming services and TV channels which air the show.
Jackson voiced a character in the episode, which aired in 1991, but his involvement was only confirmed years later.
Jackson voiced Leon Kompowsky, who meets Homer in a psychiatric hospital, where he claims to be the pop star and does the moonwalk.
“It feels clearly the only choice to make,” executive producer James L Brooks told The Wall Street Journal.
Fellow executive producers Matt Groening and Al Jean agree with the decision, he said, adding: “The guys I work with - where we spend our lives arguing over jokes - were of one mind on this.”
“This was a treasured episode. There are a lot of great memories we have wrapped up in that one, and this certainly doesn’t allow them to remain,” Brooks told the newspaper.
“I’m against book burning of any kind. But this is our book, and we’re allowed to take out a chapter,” he added.
The Jackson family have denied the allegations against the late singer, saying the HBO and Channel 4 film is “all about the money”.