Referee Kevin Friend sent Pardew to the stands at the KC Stadium after Meyler reacted angrily to the incident, with players and officials needed to separate the pair.
The Magpies boss apologised immediately after the game for his actions, while the club fined him 100,000 pounds and issued him a formal warning on Sunday.
Pardew is expected to receive a lengthy ban following the incident, and the FA confirmed on Monday afternoon on its official Twitter account that he has been charged.
Newcastle manager Alan Pardew charged with improper conduct http://t.co/JHkipOQyJA— The FA (@FA) March 3, 2014
A statement released on the governing body's official website added: “Newcastle United manager Alan Pardew has been charged in relation to an incident in his side’s game against Hull City on 1 March 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 GMT on Thursday 6 March 2014 to respond to the charge.”
The incident comes just two months after the FA reminded Pardew about his responsibilities following a foul-mouthed tirade at Manchester City boss Manuel Pellegrini.