The 50-year-old was dismissed from the touchline during his side's 5-1 defeat against Newcastle United on Boxing Day for his reaction to Glenn Whelan's red card
Hughes was sent to the stands during the first half of Stoke's 5-1 defeat at St James’ Park for his reaction to Glenn Whelan’s red card after the midfielder challenged Yohan Cabaye.
An FA statement read: "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."
Whelan and Marc Wilson will both serve one-match bans for their red cards against Newcastle and will miss Sunday’s fixture against Tottenham at White Hart Lane.
Hughes will likely face a financial penalty, rather than a touchline ban, if he accepts the charge or is found guilty by the FA.