The Liverpool captain was shown a straight red card in the 29th minute at St James’ Park on Sunday for fouling Newcastle forward Alexander Isak.
The defender appeared to argue with referee John Brooks while the incident was reviewed by VAR.
The FA says it is alleged Van Dijk used “abusive and/or insulting words”.
“Virgil van Dijk has been charged with a breach of FA rule E3.1 following Liverpool’s Premier League game against Newcastle United on Sunday, 27 August,” said the FA in a statement.
“It’s alleged that the defender acted in an improper manner and/or used abusive and/or insulting words towards a match official after being sent off in the 29th minute.”
The 32-year-old Netherlands centre-back, who also appeared to argue with the fourth official before making his way down the tunnel, has until Friday to respond to the charge.
Currently, Van Dijk will serve a one-match ban for the initial red card and miss Liverpool’s next game against Aston Villa on Sunday.
The charge comes after referees’ chief Howard Webb said he was “determined” officials would not “turn a blind eye” to bad behaviour from players and coaches this season.
The incident occurred three minutes after Liverpool went behind to Anthony Gordon’s opening goal and with the visitors under pressure in the game.
Darwin Nunez came off the bench to score twice late on and hand Liverpool a 2-1 victory to maintain their unbeaten start to the season.
