McClaren has until 15th December to respond to the charge, which was brought after he marched onto the pitch to remonstrate with match referee Phil Dowd, following Franck Queudue's first half dismissal.
The Boro boss could face a touchline ban if the charge is upheld.
French Franck has been hit with a three match ban after his dismissal and will miss the games against Manchester City, Southampton and Aston Villa. George Boateng will also miss the Manchester City game after picking up his fifth yellow card of the season.