Trouble broke out in the Millwall supporters' section during the team's 2-0 loss to Wigan.
A 43-year-old man was charged with racially aggravated behavior while another 53-year-old was charged with breaching bail conditions.
The former will appear before Hendon magistrates on May 1.
Detective Chief Inspector Andy Barnes said in a statement: "The violence seen at the Millwall v Wigan FA Cup fixture over the weekend is completely unacceptable.
"A significant investigation is now under way to identify all involved in order to bring them to justice in a swift and robust manner."