"Manchester City's Gareth Barry has been charged by The FA for a breach of its Rule E3 in that he used abusive and/or insulting words towards a match official following the Manchester City v Manchester United game on Sunday 9 December 2012," a statement on the FA's website said on Tuesday.
The England midfielder has until 1600 GMT on Thursday to respond to the charge.
The match, won 3-2 by United, was marred by crowd trouble following Robin van Persie's late winner at the Etihad Stadium.
Police are trying to identify a supporter who threw a coin at United defender Rio Ferdinand which left him bleeding from a cut about his left eye.
As he was recovering, City fan Matthew Stott ran onto the pitch and tried to reach him, but was restrained by the home side's goalkeeper Joe Hart.
He was one of two people charged with pitch encroachment.
In total 13 people were arrested after the match, with nine being charged including one for a racially aggravated public order offence.
City have since apologised to Ferdinand, and the FA is investigating the incident.
Professional Footballers' Association boss Gordon Taylor has since suggested netting should be erected in some parts of stadiums to protect players from objects being hurled from the crowd, while the FA's chairman David Bernstein has said fans who "hijack" matches with bad behaviour should be banned for life.
English football, long seen to have dealt with previous problems with hooliganism and racism, has been hit by a series of recurrences in recent times.
