Wigan appointed former Cardiff City boss Malky Mackay as manager last week, a decision that attracted criticism after the Scot was reported to the FA over his exchange of text messages with Iain Moody - former head of recruitment at Cardiff.
Mackay admitted the messages were "disrespectful of other cultures" and he has come under investigation from the FA.
In the aftermath of the appointment, Whelan gave an interview to The Guardian, where he suggested there was not "a lot wrong" with anything Mackay had said in those messages.
The 77-year-old was forced to apologise for this comments, but he provoked widespread outrage when he described Jewish people as "chasing money more than everybody else".
The FA confirmed last week that it had contacted Whelan regarding his remarks and a statement released on Thursday declared that he had been charged.
"The FA has charged Dave Whelan in relation to media comments," a statement read.
"It is alleged the Wigan Athletic chairman breached FA Rule E3 in that his comments were abusive and/or insulting and/or constitute improper conduct and/or bring the game into disrepute.
"It is further alleged that this is an 'Aggravated Breach' as defined by FA Rule E3 as it included a reference to ethnic origin and/or race and/or nationality and/or religion or belief.
"Mr Whelan has until 6pm on 5 December 2014 to respond to the charge."
Whelan has previously indicated that he would resign if found guilty of any offence.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.