The charge relates to his celebrations following Rio Ferdinand's last-gasp winner in the 1-0 win against Liverpool at Old Trafford on Sunday.
The FA's action, based on referee Mike Riley's report, comes after Greater Manchester Police expressed concerns over Neville's behaviour.
England international Neville, 30, has until 10 February to respond.
Refereee Riley failed to see the incident but offered his verdict on Neville's actions after reviewing video footage.
Neville was seen to grab his shirt and gesticulate wildly towards Liverpool fans after Ferdinand's late winner.
The England defender was initially unapologetic about his behaviour.
He said: "I would have been apologetic if I had run up to one of their players and tried to belittle them, but this was a celebration.
"You are caught up in the moment and for a few seconds you go bananas.
"I laughed when I heard someone say it was not the behaviour of a 30-year-old because they are probably the same people who have accused us of lacking passion in recent games."
As the case is not on the FA's new fast-track disciplinary process, Neville may escape with just a heavy fine.