Video footage showed Ronaldo appearing to knock a fan’s mobile phone to the ground after United’s 1-0 defeat at Goodison Park on April 9, for which the Portuguese was cautioned by Merseyside Police.
Now the FA has decided to probe the incident and a spokesperson said on Twitter: "Cristiano Ronaldo has been charged with a breach of FA Rule E3 for an incident that took place after Manchester United FC’s Premier League match against Everton on Saturday 9 April 2022.
"It is alleged that the forward’s conduct after the final whistle was improper and/or violent."
After the incident, which occurred when Ronaldo was making his way towards the tunnel, the 37-year-old issued a social-media apology for his "outburst" and invited the supporter to watch a game at Old Trafford "as a sign of fair play and sportsmanship".
Taking to his Instagram account after the match, the Portuguese forward said: "It’s never easy to deal with emotions in difficult moments such as the one we are facing.
"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."
In response to the charge against Ronaldo, who has started just once under Erik Ten Hag in the Premier League this season, United said in a statement: "We will be supporting the player."
Additional reporting from PA