Pardew, 52, has until 6pm on Thursday to respond to the charge, 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."
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 after the match suggests he has little alternative - or be found guilty, he could face significant punishment, which could even amount to a stadium ban.
The allegation is that Pardew head-butted Meyler after the player collided with him on the touchline in pursuit of the ball during Newcastle's 4-1 victory at the KC Stadium.
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 the Hull manager, Steve Bruce, although Newcastle announced within hours that they had fined Pardew £100,000 and given him a formal warning.
Newcastle said in a statement: "Newcastle United are disappointed with the actions of their manager Alan Pardew. His behaviour was unacceptable and is not the behaviour we expect from the manager of Newcastle United."
However, Mike Ashley, the owner, stopped short of relieving Pardew of his duties. Newcastle are eighth in the Premier League table after back-to-back wins.
The manager will not face police action either. Humberside Police said neither Meyler nor his club had made a formal complaint.
Chief Inspector Rich Kirven said: "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.
"While we appreciate 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. He trained with their squad in Malahide yesterday morning.