Saturday's game, which Wigan won 2-0, was marred by violent scenes inside and outside London's Wembley Stadium.
Today, Scotland Yard said Richard Freeman, 53, of Grebe Way, St Neots, Cambridgeshire, had been charged with breaching bail conditions.
He appeared in custody on Monday, police said.
Terance Cape, 43, of Goldwin Close, New Cross, London, will appear on bail at Hendon Magistrates' Court on May 1 charged with racially aggravated behaviour under section 4 of the Public Order Act.
Fourteen people were arrested on Saturday, police said, 12 Millwall supporters and two Wigan fans.
Detective Chief Inspector Andy Barnes said: "The violence seen at the Millwall v Wigan FA Cup fixture over the weekend is completely unacceptable.
"The Metropolitan Police is committed to working with its partners in bringing those responsible to justice.
"A significant investigation is now under way to identify all involved in order to bring them to justice in a swift and robust manner."