The Gunners boss branded the VAR decision not to rule out Anthony Gordon's goal in his side's 1-0 defeat at St James' Park "an absolute disgrace".
An FA statement read: "Mikel Arteta has been charged with a breach of FA Rule E3.1 following comments that he made in media interviews after Arsenal's Premier League game against Newcastle United on Saturday, November 4.
"It's alleged that his comments constitute misconduct as they are insulting towards match officials and/or detrimental to the game and/or bring the game into disrepute."
VAR made a triple check to see whether the ball had gone out of play before Joe Willock's cross, whether Joelinton had fouled Arsenal defender Gabriel and whether Gordon had been offside.
Arteta could not hide his anger after the match, saying: "You have to talk about how the hell did this goal stand up? Incredible. I feel embarrassed.
"I have to now come in here and try to defend the club and please ask for help because it's an absolute disgrace that this goal is allowed. An absolute disgrace."
Arsenal issued a statement the following day saying the club "wholeheartedly" supported Arteta's comments.
"The Premier League is the best league in the world with the best players, coaches and supporters, all of whom deserve better," said the statement.
"PGMOL (Professional Game Match Officials Limited) urgently needs to address the standard of officiating and focus on action which moves us all on from retrospective analysis, attempted explanations and apologies."
Arteta has until Tuesday to respond to the charge.