The Jake the Peg artwork was painted backstage when Harris carried out a week-long stint at the Adam Smith theatre in Kirkcaldy in 1985.
The 84-year-old was jailed last week for five years and nine months after he was found guilty of 12 charges of indecently assaulting four girls between 1968 and 1986.
The mural, painted in a corridor connecting the stage to the dressing rooms, features a cartoon of three-legged Harris wearing a kilt alongside phrases such as "There's nowt that's shoddy about Kirk-coddy."
In a written message to staff, he said: "Well, I can't recall when I've been made to feel as welcome. We'll come back anytime. Thanks again, Rolf Haggis."
Laurie Piper, of Fife Cul-tural Trust, said: "We are in the process of decorating, refreshing and updating a number of areas in the theatre, and in light of recent developments and the sensitivity of having performers of all ages, we believe it appropriate to remove the caricature."
But Bert Ross, who was in charge of publicity and oversaw Harris' tenure in 1985, said: "It's a part of the theatre's history and perhaps should be left there."