The Chelsea star will face action for a comment which was "improper and/or brought the game into disrepute" after lashing out at the national body on the social networking website.
Cole attacked the FA's Independent Regulatory Commission after they found his teammate John Terry guilty of racially abusing Anton Ferdinand and questioned the credibility of the evidence the left back gave as a witness.
The England international labelled the FA a "bunch of t****" but later deleted the tweet and apologized "unreservedly" for comments he made "in the heat of the moment".
Cole, who was been capped 98 times, was included in the Three Lions squad to face San Marino and Poland in the upcoming World Cup qualifiers and remains a part of Roy Hodgson's group for the two fixtures.
An FA statement reads: "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 has until 4pm on Thursday 11 October 2012 to respond to the charge."
Chelsea manager Roberto Di Matteo has already confirmed that Cole will face club disciplinary action in accordance with the Stamford Bridge side's social media policy.
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