Fulham's Sascha Riether has become the first player to be charged under a new retrospective action scheme.
The defender, 30, appeared to stamp on Manchester United's Adnan Januzaj in Fulham's 3-1 loss, but match officials did not see the incident.
Under the new rules, a three-man panel of former elite referees looked at the incident and advised Reither committed an act of violent conduct.
Riether has until 1800 GMT on 5 November to respond to the charge.
Previously retrospective action could previously only be taken when one of the officials had seen it or in exceptional circumstances.
But the new scheme was introduced after Wigan's Callum McManaman escaped punishment for a dangerous tackle on Newcastle defender Massadio Haidara last season.
"For an FA charge to follow all three panel members must agree it is a sending-off offence," the FA said. "In this instance, the panel were of the unanimous decision that it was an act of violent conduct."
Callum McManaman's tackle on Massadio Haidara
Massadio Haidara said the decision not to punish Callum McManaman for this challenge last season was "ridiculous"
Speaking before being made aware of the FA charge, United manager David Moyes called for more protection for his 18-year-old winger.
He said: "It is a bad stamp and it does look deliberate.
"I do think Adnan is going to need a little bit of protection or we are going to find that he is getting kicked up and down. It is not a case of asking for protection.
"We are just saying that somewhere along the line, people will need to let the boy, if he is going to keep playing in the fashion and style we want, he is going to have to get some protection from it."