The United boss has been charged with improper conduct for the comments he made following the 2-2 draw between the two side's earlier this month at Old Trafford.
"Manchester United manager Sir Alex Ferguson has been charged with improper conduct," the FA said in a statement.
"The charge relates to media comments made by Ferguson about referee Alan Wiley following United's match against Sunderland at Old Trafford on 3rd October."
Fergie has until 3rd November to answer the charge.