The charge relates to an incident in Saturday's 1-0 loss at Bury.
The FA alleges that the 48-year-old used "abusive and/or insulting and/or improper words and/or behaviour towards a match official" around the tunnel area at half-time.
The former Tottenham and Aston Villa boss has until 20 February to respond.
Swindon have won three, drawn four and lost 11 of their 18 games in all competitions since Sherwood's arrival on 10 November, leaving them 22nd in League One.
Swindon Town director of football Tim Sherwood has been charged by the Football Association for allegedly abusing a match official.