Moyes, 54, made the remark, for which he has apologised, to BBC reporter Vicki Sparks following Sunderland's 0-0 draw with Burnley in the Premier League on March 18.
"David Moyes has been charged in relation to comments made after the game against Burnley on 18 March 2017," the FA said in a statement.
"It is alleged the Sunderland manager's remarks were improper and/or threatening and/or brought the game into disrepute."
Moyes, the former Manchester United manager, has until Wednesday next week to respond to the charge.
Should he admit the charge or be found guilty, he is likely to be fined and could be asked to attend an education course.
Moyes made his remark at the end of a post-match interview, but the camera was still rolling and footage was published weeks later by a British newspaper.
Having taken exception to one of Sparks' questions, Moyes said: "You were just getting a wee bit naughty at the end there, so just watch yourself. You still might get a slap, even though you're a woman.
"Careful the next time you come in."
Moyes later apologised in a phone call to Sparks, who did not make a complaint.
"In the heat of the moment, I made a mistake in my comments to a BBC reporter, which I profoundly regret. I was disappointed with myself for it," Moyes said.
"I subsequently phoned the reporter and apologised, which she accepted. It's not my character, it's not my type, as most people know and once again I apologise for it."
Sunderland are currently 12 points adrift of safety at the foot of the table and seemingly doomed to relegation.