Footage posted on social media appeared to show a section of the club's supporters taunting away fans by using a derogatory term about the Pakistani community.
The FA launched an investigation into the incident and confirmed the Championship side has now been charged.
"Millwall FC has been charged with a breach of FA Rule E20," said an FA statement.
"It is alleged the club failed to ensure its spectators conducted themselves in an orderly fashion and refrained from using abusive and/or insulting words, which included a reference to race and/or ethnic origin, during the FA Cup tie against Everton on January 26."
Following the game, which Millwall won 3-2 to stay on course for a quarter-final at home to Brighton and Hove Albion, the club condemned the alleged racist abuse as "abhorrent".
"Millwall Football Club is aware of, and extremely disappointed by, a video circulating online displaying alleged racist chanting during Saturday's victory over Everton," a Millwall statement read.
"The club will, as is commonplace following such incidents, work with all relevant authorities during investigations into the matter and look to identify individuals involved. Anyone identified and guilty of such abuse will be banned from The Den for life."
Before the match, Everton fan Jay Burns was attacked and suffered a facial gash that required 25 stitches.
Police arrested and bailed a 27-year-old man on suspicion of wounding with intent, attempted grievous bodily harm and violent disorder.