The England left-back later deleted the tweet but only after it was re-tweeted more than 19,000 times, and then made a full apology.
But that did not stop the FA taking action, in addition to disciplinary proceedings already taken by his club.
A statement on the FA's website said: "Chelsea FC's Ashley Cole has been charged by The FA in relation to a Twitter comment which was improper and/or brought the game into disrepute."
Cole, who is in England's squad for Friday's World Cup qualifier against San Marino at Wembley, has until 1500GMT on Thursday to respond to the charge.