The charge relates to an incident during his side's Barclays Premier League match against Sunderland on Saturday, and he now has until 4pm on Thursday to respond to it.
A statement from the FA read: "Aston Villa coach Kevin MacDonald has been charged by the FA for using language and/or behaviour amounting to improper conduct."
The FA said that MacDonald had been sent to the stands during the second half of the match, with reports from the day suggesting his ejection followed a protest to the fourth official against a decision made by match referee Chris Foy.
Source: PA
Source: PA