Fourteen people were arrested following violence at the FA Cup semifinal between Wigan and the Lions in scenes described as 'unacceptable' by the Football Association.
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."