The FA said those chants can have a "lasting and damaging impact" on people and communities within the game and must be stopped.
"This important step follows the recent successful prosecution of an individual by the Crown Prosecution Service for homophobic abuse, specifically relating to the term 'Rent Boy'," the FA said.
"The FA has now informed all clubs that it considers the 'Rent Boy' chant to be a breach of the FA Rules.
"These rules apply to the conduct of supporters at both home and away fixtures, and clubs at all levels of English football have a responsibility to ensure their spectators behave appropriately when attending matches."
The statement came days after the FA said it would open an investigation after supporters were heard using homophobic language towards Everton manager Frank Lampard during his team's 3-1 FA Cup loss at Manchester United.
