The Scot was critical of Wiley during the 2-2 draw with Sunderland at Old Trafford on October 3 but is now facing a touchline ban.
After the game, Ferguson blasted: "The pace of the game demanded a referee who was fit. He was not fit. It was ridiculous."
Ferguson subsequently apologised for causing any embarrassment to Wiley but it was criticised for being "half-hearted".
An FA statement read: "The charge relates to media comments made by Ferguson about referee Alan Wiley following United's match against Sunderland at Old Trafford on 3 October."
Ferguson has until 3 November to respond to the charge.