The Creggan born winger, 30, does not wear a poppy on his shirt for the games scheduled around Remembrance Day over the murder of 13 innocent people on Bloody Sunday in January 1972 by British soldiers.
Barnsley have until next Friday, January 10, to respond to the charge.
They said in a statement: “Barnsley Football Club has a zero tolerance policy on any form of discrimination.
“As a club, we are saddened to have had this charge brought against us.
“We will await and respect the outcome of the FA’s charge against us before communicating further on this matter.”
The Potters won the game at Oakwell 4-2.
On Wednesday, an announcement was made over the public address system at Huddersfield warning fans about “offensive behaviour” affecting the game between the Terriers and Stoke after it was alleged that sectarian chants were aimed at Republic of Ireland international McClean.
James applauded the announcement and his manager Michael O’Neill condemned those behind the racial abuse of his star player.
The Professional Footballers’ Association has said it plans to hold talks with the English Football League and refereeing body Professional Game Match Officials Limited to discuss how to deal with the issue.