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It relates to an incident in April in which he appeared to slap a boy's phone out of his hand while heading down the tunnel at Old Trafford, following United's 1-0 defeat to Everton.
Footage of the incident was widely shared on social media alongside comments which claimed that Ronaldo had smashed the phone in anger while leaving the pitch.
The 37-year-old apologised for the "outburst" and was later cautioned by police in August.
The FA have now decided to charge the forward, who is currently away on international duty with Portugal.
"It is alleged that the forward's conduct after the final whistle was improper and/or violent," read a statement.
Manchester United issued their own statement confirming they would “support the player in his response to the charge".
Sarah Kelly, the mother of the boy involved, said her 14-year-old son, Jake Harding, had been left "bruised" and "in complete shock" by the incident.
Man Utd: “We note the FA announcement in relation to Cristiano Ronaldo. We will be supporting the player in his response to the charge."— Simon Stone (@sistoney67) September 23, 2022
Speaking to the Liverpool Echo at the time, Kelly said her son was autistic and "really upset" about what happened – claiming it had "completely put him off" attending another match.
Ronaldo later apologised on social media and invited the young supporter to watch another game at Old Trafford.
"It's never easy to deal with emotions in difficult moments such as the one we are facing," he wrote on Instagram.
"Nevertheless, we always have to be respectful, patient and set the example for all the youngsters who love the beautiful game.
"I would like to apologise for my outburst and, if possible, I would like to invite this supporter to watch a game at Old Trafford as a sign of fair-play and sportsmanship."
Ronaldo is currently away with Portugal as they prepare for their upcoming Nations League matches against Czech Republic on Saturday and Spain on Tuesday.
United return to action after the international break against rivals Manchester City at the Etihad on October 2.
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