Footage showed Ronaldo appearing to knock a fan's mobile phone to the ground after United's 1-0 defeat at Everton on April 9, for which the Portuguese was cautioned by Merseyside Police.
"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," said a FA spokesperson.
"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".
If found guilty of the charge, Ronaldo could face a ban from upcoming Premier League matches.
The five-time Ballon d'Or winner has only started in the league once this season under Erik ten Hag after failing to force a move away from Old Trafford during the transfer window.
In a statement, United said: "We note the FA announcement in relation to Cristiano Ronaldo.
"We will be supporting the player in response to the charge."
