The Belgian clashed with the England international on many occasions during the 1-1 draw between the sides on Saturday, and the FA have confirmed that the midfielder has been charged retrospectively.
Referee Mark Halsey confirmed that he had not seen the incident in the 59th minute where Fellaini headbutted his opponent, but stated that he saw two further incidents where the midfielder appeared to elbow Shawcross in the 71st minute before pushing him in the face in the 91st minute and deemed neither to be violent conduct.
|HEADBUTT UNACCEPTABLE - MOYES
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Fellaini has already apologised for the incident, stating: "I apologise completely to Ryan Shawcross, my team-mates and to our fans at the game.
"There was a lot of pushing and pulling going on inside the Stoke penalty area and I didn't feel I was getting any protection from the officials.
"Nevertheless I know I shouldn't have done what I did.
"I have also apologised to the manager and the staff. I have no excuses, I was disappointed with the way I was being treated and I lost my temper, which was unprofessional of me."