"It is alleged the comment posted on his twitter account was abusive and/or indecent and/or insulting and/or improper," the governing body said in a statement.
"It is further alleged that this breach is aggravated pursuant to FA Rule E3(2) as it included a reference to gender."
The Queens Park Rangers defender, 35, has until Oct. 21 to respond to the charge.
According to British media reports, the alleged offensive Tweet was sent in September.
Ferdinand was tagged in a message that read: "Maybe QPR will sign a good CB (centre back) they need one."
In response, he tweeted: "get ya mum in, plays the field well son! #sket," a Jamaican slang word.
Ferdinand, who made 81 appearances for England, has had a difficult start at QPR who are bottom of the Premier League with four points from seven games.
(Reporting by Toby Davis; editing by Justin Palmer)
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