The Football Association announced the charge relates to comments made before the Magpies' derby away to Sunderland on August 20.
It is believed to relate to the appointment of Howard Webb as referee and his role in the match, which Newcastle won 1-0.
Pardew has until 4pm on Monday to respond.
Pardew's comments: "The referee needs to make sure he referees the game from a completely neutral point of view because Joey has been in the press a fair bit this week - more than Joey would have liked and more than I would like - and I'm sure he'll get a mention in Sunderland's game plan.
"He's a very, very good player and they'll need to stop him but I've got no qualms about throwing Joey in there, no doubts at all. But the referee will need to be astute."