Trouble broke out in the Millwall supporters' section during their sides 2-0 loss to Wigan.
A 43-year-old man was charged with racially aggravated behaviour while another 53-year-old was charged with breaching bail conditions.
The former will appear before Hendon magistrates on 1 May.
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."
The Football Association have described the events as "unacceptable" while Sports minister Hugh Robertson described the scenes as "incredibly disappointing and quite depressing".
Millwall CEO Andy Ambler also says the club are "determined" to see justice brought to the fans who brawled in the stands at Wembley.