A commission will hear the case on Wednesday with the 27-year-old facing a three-match ban if found guilty.
An FA statement said: "Newcastle United defender Mike Williamson has denied a charge of violent conduct.
"The charge relates to an incident involving Johan Elmander in his side's fixture with Bolton Wanderers on Saturday, 20 November.
"A Regulatory Commission will hear the charge on Wednesday, 24 November."
If the FA uphold the ban they could increase it to FOUR matches.