Hughes was sent to the stands in his side's 5-1 Barclays Premier League loss at St James' Park.
A FA statement read: "Stoke City manager Mark Hughes has been charged by The FA following his side's game at Newcastle United yesterday.
"It is alleged that his behaviour in or around the 40th minute of the fixture amounted to improper conduct.
"Hughes has until January 2, 2014 to respond to the charge."
If he accepts the charge or is found guilty, Hughes faces a financial penalty in a standard case and no touchline ban.
Chelsea boss Jose Mourinho was punished similarly for his dismissal against Cardiff earlier this season.
Hughes' charge relates to his conduct on the touchline and not his post-match comments.
The Welshman was ordered from the dug-out after he reacted in fury to the dismissal of midfielder Glenn Whelan, and he was still making his way to his new vantage point when defender Marc Wilson followed inside three dreadful first-half minutes with the visitors leading 1-0.
Whelan picked up two yellow cards, the first for kicking the ball away and clashing with Yohan Cabaye after being penalised for a foul on Moussa Sissoko, and the second for a foul on Cabaye.
Wilson followed for hauling down Loic Remy inside the box and although goalkeeper Thomas Sorensen saved the resulting spot-kick, the writing was on the wall for the numerically-disadvantaged Potters.
Following the match Hughes hit out at referee Martin Atkinson.
He 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."