Last month Chelsea sent an email to supporters confirming that it received reports that a 'small portion' of the travelling fans engaged in sectarian chanting.
In the 3-2 victory at Craven Cottage, some Chelsea fans belted out the song Flute for 50 Pence which includes the line: "F*** the Pope and the IRA."
As per the BBC, the Blues said they do not condone any discriminatory chants, and that fans found guilty would face "the strongest possible action".
Now, a statement from an FA spokesperson read: "Chelsea FC has been charged with breaching FA Rule E21 during the ninth minute of its Premier League fixture against Fulham FC on 24 August.
"It's alleged that the club failed to ensure its spectators and/or supporters did not behave in an improper, offensive, abusive or insulting way.
"It's further alleged that this behaviour was discriminatory in that it included a reference, whether express or implied, to religion or belief."
Chelsea have only picked up one more Premier League win since overpowering Fulham and they entered the international break following a 3-0 loss to Brentford.
The West London side sit 10th in the table and next face Bournemouth at Stamford Bridge as manager Xabi Alonso aims to get his side back and track with 3 points that could launch the side back into the top 6.