Cavani, 33, reposted a message to a friend after scoring twice in the 3-2 win at Southampton on Nov. 29. He wrote in Spanish, "gracias, negrito" -- a term that can be interpreted as racist in the United Kingdom.
Although it is widely used as a term of endearment in South America and the Caribbean, the word is regarded in England, as well as within parts of the Afro Uruguayan community, as carrying racial connotations, prompting the FA to investigate Cavani's post.
If Cavani, who has missed United's past two games through injury, is found guilty, he could be hit with a three-game ban under FA rules.
A statement released by the FA on Thursday read: "Edinson Cavani has been charged with misconduct for a breach of FA Rule E33 in relation to a social media post on Sunday, Nov. 29 2020.
"It is alleged that, contrary to FA Rule E3.1, a comment posted on the Manchester United FC player's Instagram page was insulting and/or abusive and/or improper and/or brought the game into disrepute.
"It is further alleged that the comment constitutes an 'Aggravated Breach', which is defined in FA Rule E3.2, as it included reference, whether express or implied, to colour and/or race and/or ethnic origin.
"The striker has until Monday, Jan. 4 2021 to provide a response to the charge."
Sources have told ESPN that in Cavani's representations to the FA, he insisted the word is not used with racial or derogatory intent in Uruguay and that the friend in question uses the term with his own son.
United, meanwhile, argued that the word was used as a term of affection and that cultural context is key, but sources have told ESPN it was not taken into consideration by the FA.
A club spokesperson said: "Manchester United and all of our players are fully committed to the fight against racism and we will continue to work with the FA -- along with other governing bodies and organisations, and through our own campaigns -- in that regard.
"We note the FA decision today to charge Edinson Cavani for his social media reply to a friend's message of congratulations following the Southampton game.
"Edinson and the club were clear that there was absolutely no malicious intent behind the message, which he deleted and apologised for as soon as he was informed that it could have been misconstrued.
"The player and the club will now consider the charge and respond to the FA accordingly."