Huth appeared to strike Upson with his arm when the two tussled at a free-kick and the Hammers defender required treatment on a cut above his eye which had been reopened.
The incident was missed by referee Martin Atkinson but after watching video evidence he appears to have indicated to the FA that he would have dismissed Huth had he been watching.
"Stoke City defender Robert Huth has been charged with violent conduct," read an FA statement. "The charge relates to an incident involving Huth and West Ham defender Matthew Upson during the Premier League match on Saturday 17 October.
"Huth has until 6pm on Tuesday 20 October to respond to the charge. A Regulatory Commission will consider the charge on Thursday 22 October."
Huth could be facing a three-match ban if found guilty, potentially ruling him out of the upcoming Premier League fixtures against Tottenham, Wolves and Hull.