The 52-year-old has until 6pm on Thursday to respond to the charge, which has been described in an FA statement as "non-standard".
The statement said: "Newcastle United manager Alan Pardew has been charged in relation to an incident in his side's game against Hull City on March 1, 2014.
"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, March 6 2014 to respond to the charge."
Designating the alleged offence as "non-standard" means there is no real precedent and that it cannot be treated in the same way as other more common disciplinary matters.
As a result, there is no prescribed punishment and should Pardew admit the charge - his swift apology afterwards suggests he has little alternative - or be found guilty, he could find himself hit with a significant penalty which could even amount to a stadium ban.
The allegation is that Pardew head-butted Meyler after the player had collided with him on the touchline in pursuit of the ball during Newcastle's 4-1 Barclays Premier League victory at the KC Stadium on Saturday.
Meyler was cautioned by match referee Kevin Friend for his part in the incident before Pardew was ordered to the stands.
He was contrite after the game and his apology was accepted by Tigers counterpart Steve Bruce.
However, that cut little ice with his employers, who within hours announced they had fined him £100,000 and handed him a formal warning.
In their statement, the Magpies said: "Newcastle United are disappointed with the actions of its manager Alan Pardew this afternoon.
"His behaviour was unacceptable and is not the behaviour we expect from the manager of Newcastle United."
However, owner Mike Ashley stopped short of relieving Pardew of his duties, with the club sitting in eighth place in the Premier League table after back-to-back wins.
The manager will not face police action either after Humberside Police revealed that neither Meyler nor his club had made a formal complaint.
Chief Inspector Rich Kirven said in a statement: "We have been working with the FA and the football club to progress the matter appropriately.
"Having reviewed the circumstances of the incident, it has been agreed that the matter will be dealt with by the FA rather than considering any criminal proceedings.
"There has been no complaint received from the player involved or Hull City Association Football Club at this time.
"Whilst we appreciate that some people may have found the behaviour displayed at the game on Saturday offensive, Humberside Police will not be taking any further action."
Meyler, who was praised by Bruce for his restraint in the wake of the incident, is currently on international duty with the Republic of Ireland, where he trained in Malahide on Monday morning.