The move comes following Stoke's 5-1 Premier League thrashing at Newcastle United on Thursday, which saw the visitors concede two penalties and end the match with nine men - Glenn Whelan and Marc Wilson both sent off.
Hughes was also sent to the stands during the encounter as he protested against midfielder Whelan's dismissal for two bookings, and now looks set to face disciplinary action.
A statement from the FA 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."
Stoke are back in action on Sunday with a trip to White Hart Lane to face Tottenham.
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