The FA, as expected, hit the 52-year-old with the charge on Monday afternoon after an incident on the touchline at the KC Stadium on Saturday.
An FA 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."
The allegation is that Pardew headbutted 24-year-old Hull midfielder Meyler as they clashed on the sideline during the Magpies' 4-1 Barclays Premier League victory.
Newcastle have already fined their manager £100,000 and handed him a formal warning but should he admit or be convicted of the offence, he will face further punishment by the FA.
The fact that the matter has been designated "non-standard" means it is out of the ordinary and that there is no precedent for dealing with similar incidents.
By extension, there is no fixed penalty and there is a possibility that Pardew could face a stadium ban.
However, the 52-year-old will not be subject to a police investigation over his behaviour at the weekend.
Humberside Police have confirmed that neither Meyler nor the Tigers have made a complaint, and that therefore they will leave matters to the FA.
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."
While Pardew considers his options, Meyler is on international duty with the Republic of Ireland, who face Serbia in Dublin on Wednesday night.
Asked how the player was after training on Monday, assistant manager Roy Keane said: "He's fine. You have seen him training, he's having a good season for Hull and it's good to have him involved."