The German center back could face a three-game suspension following a clash with Philippe Senderos during the club's match against Fulham in the Premier League on Saturday.
Huth clashed with Cottagers defender Philippe Senderos during the Potters' 1-0 defeat, although referee Lee Probert did not see the incident.
However, the FA has acted retrospectively and given Huth until Tuesday night to respond to the charge.
If he is handed a suspension, he is likely to miss his side's next three matches - Premier League games against West Ham, Newcastle and West Brom.
The 28-year-old has been a regular once again under Tony Pulis this season - making 27 appearances and scoring once in the league so far.
Stoke midfielder Steven N'Zonzi clashed with Dimitar Berbatov and Bryan Ruiz in separate incidents during the game, though neither will require further action.