The England international was unavailable for the match as he recovers from a hamstring injury.
James is alleged to have confronted referee Jarred Gillett following the Blues' disappointing 1-0 loss at Stamford Bridge - their third defeat in the Premier League already this season.
Chelsea went down to 10 men in the second half of the match after defender Malo Gusto was sent off in the 58th minute for dangerous play.
VAR recommended referee Gillett review the incident on the pitchside monitor which led to the Frenchman's dismissal.
The FA said in a statement: "Reece James has been charged with a breach of FA Rule E3 following Chelsea's Premier League game against Aston Villa on Sunday, September 24th.
"It's alleged that the defender used improper and/or insulting and/or abusive words and/or behaviour towards a match official in the tunnel after the game."
The right back has until September 29th to respond to the charge.
The loss leaves boss Mauricio Pochettino under increasing pressure, with Chelsea languishing in 14th place and already 13 points adrift of league leaders Manchester City.
