Pardew has already been sanctioned by Newcastle, accepting a formal warning and a 100,000 pound ($168,000) fine following his confrontation with Hull midfielder David Meyler on Saturday. But any FA punishment could prevent Pardew from attending several matches, rather than just being banned from the touchline.
"Due to the serious violent and/or aggressive nature of the reported behaviour this case has been designated as non-standard," the FA said in a statement.
Pardew, who has already apologized, has until Thursday evening to respond to the charge. Earlier this season, then-Blackpool manager Paul Ince received a five-match stadium ban from the FA for violently shoving a fourth official in an expletive-laden rant.
Pardew's confrontation at the KC Stadium happened in the 72nd minute. Meyler initially barged into Pardew as he looked to retrieve the ball for a throw-in. After squaring up to Meyler before moving his head in the direction of the player's face, Pardew was sent to the stands.
Newcastle beat Hull 4-1.