Deeney came to blows with Stoke City’s Joe Allen during the 1-0 defeat at Vicarage Road on Saturday.
The Watford forward appeared gauged his thumb into Allen’s cheek as the pair engaged in a heated on-field argument.
Both players received a yellow card at the time of the incident by referee Michael Oliver.
However, the FA have deemed it appropriate to take further action against the 29-year-old.
An FA statement read: ”Watford's Troy Deeney (has been) charged with violent conduct following Stoke City match on 28/10/17 and has until 18:00 on 31/10/17 to respond."
Troy Deeney has been served with a three-match ban
Deeney came to blows with Allen at Vicarage Road
I’ve seen pictures of raised hands and thumbnails in faces and that’s not really necessary.
Stoke boss Mark Hughes was furious with the incident
Deeney will sit out of the Hornets’ Premier League matches against Everton, West Ham and Newcastle.
Stoke boss Mark Hughes said after the game: "I’ve seen pictures of raised hands and thumbnails in faces and that’s not really necessary.
"I thought it was a bit unnecessary, if truthful. Clearly we kicked the ball out and the right thing to do in the spirit of the game is throw it back.
"Deeney, the captain of the club, should know better but he shaped to play it into our box and that's why Joe reacted.
Deeney had to be dragged away from Allen by his team-mate
"More often than not those situations get revisited by people in authority and decisions are made as a consequence."
However, Allen tried to play down the incident after the game, saying: “It was handbags really and there was nothing to it. I like Troy, he's one of the good guys. It was nothing personal.”
Deeney has a notorious bad reputation after he controversially returned to professional football after spending time in jail.
The Birmingham-born striker was sentenced to 10-months behind bars in September 2012 following a conviction for affray.