Barton was sent off for elbowing Carlos Tevez and then kicked Sergio Aguero before attempting to headbutt Vincent Kompany.
The FA statement: "The FA has today charged Queens Park Rangers midfielder Joey Barton in relation to two acts of alleged violent conduct during Sunday's match against Manchester City at the Etihad Stadium.
"Following the player's dismissal in the 54th minute of the fixture, there followed two incidents involving Manchester City's Sergio Aguero and Vincent Kompany.
"As Barton had already been dismissed, both of these incidents fell outside of the jurisdiction of the referee."
Barton has until 6pm on Tuesday to respond to the charges.