The Potters took the lead at St James' Park but ended up being hammered 5-1 by their hosts - finishing the game with nine men following red cards for Glenn Whelan and Marc Wilson.
The first-half dismissal of Republic of Ireland midfielder Whelan sparked some heated debate on the touchline, resulting in referee Martin Atkinson asking an irate Hughes to watch the rest of the game from the stands.
A statement on the FA website read: "Stoke City manager Mark Hughes has been charged by The FA following his side's game at Newcastle United yesterday [Thursday 26 December].
"It is alleged that his behaviour in or around the 40th minute of the fixture amounted to improper conduct."
Hughes has until 2 January 2014 to respond to the charge.
In the wake of the game, Hughes said: "From one of our arguably most senior referees, I was absolutely dismayed by his performance, to be perfectly honest.
"We were very much in control of the game and then the referee makes a couple of decisions which change the course of the game.
"We all say, managers, players, everybody, that you just want the referees to make decisions that are correct and make the key decisions that don't have a direct impact on the result.
"Unfortunately, some of Martin's decisions today had a direct impact on the result."