Video footage appeared to show Ronaldo slapping a mobile phone out of a supporter's hand as he made his way back to the dressing room.
The 37-year-old was cautioned by police in August and has now been charged with "improper and/or violent conduct" by the FA.
A statement released by the FA on Friday read: "Cristiano Ronaldo has been charged with a breach of FA Rule E33 for an incident that took place after Manchester United FC's Premier League match against Everton FC on Saturday 9 April 2022.
"It is alleged that the forward's conduct after the final whistle was improper and/or violent."
United issued a statement shortly afterward that read: "We note the FA announcement in relation to Cristiano Ronaldo. We will be supporting the player in his response to the charge."
Following the incident at Goodison Park, Merseyside Police began their own investigation, which was concluded in August when Ronaldo was issued a caution.
A statement from Merseyside Police on Aug. 17 read: "We can confirm that a 37-year-old man voluntarily attended and was interviewed under caution in relation to an allegation of assault and criminal damage.
"The allegation relates to an incident following the Everton v Manchester United football match at Goodison Park on Saturday April 9.
"The matter has been dealt with by way of conditional caution. The matter has now concluded."
Sources have told ESPN that if Ronaldo is found at fault by the FA, he could face a warning, fine or suspension.