The incident occurred during Chelsea's 2-1 loss at Emirates Stadium, where Neto was sent off after receiving two yellow cards in the same match. The game was officiated by referee Darren England.
Neto's first booking came for dissent shortly after Jurrien Timber had scored for Arsenal. The winger was later shown a second yellow card for bringing down Gabriel Martinelli in an attempt to halt a dangerous Arsenal attack. Despite protesting his innocence to the referee, Neto was eventually dismissed.
The FA alleged that he "acted in an improper manner by failing to leave the pitch promptly and/or using abusive words towards the match official/s".
The sending-off left Chelsea to play the final 20 minutes, plus stoppage time, with ten men. The red card marked Chelsea's seventh dismissal in the Premier League this season, a trend manager Liam Rosenior has described as a "deep-lying" issue within the squad.
"As a group, me as the leader as well, we have to take more accountability for some of the decision-making we're having in terms of our discipline and in terms of the moments of the goals," Rosenior said.
"Some of them are just not acceptable at this level.
"You can fine players. It's not about the punishment, it's about finding the reason why. It's a focus and a concentration thing that we need to get right.
"I know the record of the club is not great from the start of the season, and now it's getting bad. We had 10 games when I was in where we didn't have these issues, but we've had two in two games. There's something deep-lying that we need to get to the bottom of.
"The thing is, for me, if we get to the bottom of those two main things, we can be a very, very good team and we can achieve all the things we want to achieve."
Neto has until 9 March to respond to the charge. If proven, the Portuguese forward could face either an extended suspension or a fine.
He has already served the automatic one-match ban, missing Chelsea's 4-1 victory over Aston Villa - a significant win against a rival in the race for Champions League qualification.
As it stands, Neto remains eligible for Chelsea's FA Cup fifth-round tie against Wrexham this weekend and the Premier League clash with Newcastle United on 14 March.