Ferdinand escaped a booking for swinging an arm at Fagan on Saturday but has been charged retrospectively and could face a three-match ban similar to those handed out to Stoke's Robert Huth and Manchester City's Emmanuel Adebayor earlier this season.
Both Huth and Adebayor were banned for three games, with the German defender punished for an elbow to Mathhew Upson and Togo striker Adebayor reprimanded for stamping on former team-mate Robin van Persie.
An FA statement read: "Manchester United defender Rio Ferdinand has been charged with violent conduct.
"The charge relates to an incident involving Hull City forward Craig Fagan during the second half of the match at Old Trafford on Saturday 23 January.
"Ferdinand has until 6pm on Wednesday 27 January to respond to the charge. A Regulatory Commission will hear the charge on Thursday 28 January."
The match against Hull was Ferdinand's first appearance for Sir Alex Ferguson's side since the 2-0 defeat to Liverpool on October 25.