Pardew caused widespread outrage when he thrust his head into the face of Hull City midfielder Meyler during Newcastle's 4-1 victory on Saturday.
The incident followed a brief shoving exchange on the touchline as the Irishman prepared to take a throw-in.
Newcastle fined Pardew £100,000 on the evening of the incident, while League Managers Association chief executive Richard Bevan branded the 52-year-old's actions "unacceptable and insupportable" the following day.
A statement from the FA on Monday read: "It is alleged that in the 72nd minute of the fixture, Pardew was involved in an incident with a Hull City player that amounted to improper conduct.
"Due to the serious violent and/or aggressive nature of the reported behaviour this case has been designated as non-standard.
"Pardew has until 6pm on Thursday 6 March 2014 to respond to the charge."
Pardew received a two-match touchline ban last season for pushing a referee's assistant during a match against Tottenham.
Furthermore, the former Southampton boss was forced to apologise for a foul-mouthed rant at Manchester City manager Manuel Pellegrini earlier this term, which prompted the FA to "remind him of his responsibilities".
The extent of Pardew’s potential punishment for his latest transgression is as yet unclear.
‘I don’t think Liverpool would look at Ollie Watkins, a striker isn’t a pressing issue for them – it’s Arsenal who need one’ Former Reds star explains why his old club don’t need an out-and-out forward this summer
‘He’ll still be playing at 40 at a good level because he’s in such good shape and looks after himself so well. He does everything to be a top professional’: Ex-Liverpool coach insists Mohamed Salah has plenty more miles in the tank
