Cole called the FA a "bunch of twats" after having his evidence questioned by the organisation's disciplinary commission conducting an investigation into claims that his Chelsea team-mate John Terry racially abused QPR defender Anton Ferdinand.
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.
Despite Cole's evidence in support of Terry, the defender was banned for four matches and fined £220,000 after being found guilty of racially abusing Ferdinand.
Cole had said he thought Ferdinand may have used the word 'black' during the verbal exchange with Terry, which supported his team-mate's version of the incident.
But according to the FA commission, Cole did not mention the word 'black' in the initial interview with the FA on October 28 last year and the written summary of the case suggested the left-back's evidence "evolved" over time to suit Terry's defence.
Some pundits, including former England striker Alan Shearer, have called for the 31-year-old to be banned from the San Marino game and next week's trip to Poland as punishment for his tweet.
Shearer told the BBC: "I think the FA can put a big statement out here by not fining him but actually banning him on Friday against San Marino."
However, Cole has spoken to England coach Roy Hodgson, who was reportedly keen to ensure the player didn't retire from international duty in reponse to the controversy, and was due to meet up with the England squad at the FA's new national football centre, St George's Park, on Monday.
It is understood that if he is left out of the San Marino match it will be a case of Hodgson resting players against the Group H minnows rather than any statement relating to the controversy that erupted on Friday.
Cole, who has 98 England caps to his name and could reach the century mark against Poland, will also be part of the England squad that assemble at St George's Park for the official opening on Tuesday by the Duke and Duchess of Cambridge.
Chelsea boss Roberto Di Matteo had confirmed on Saturday that the former Arsenal star would be punished by his club.
"We've got a social media policy at the club and there's going to be a disciplinary process - action - against the tweet and that's how I'll leave it," Di Matteo said.
"The image of the club is very important to us of course. We have rules, and anybody who breaks the rules faces disciplinary action against them."