Gerrard Scanlon, a 53-year-old from Enfield, north London, was arrested by Metropolitan Police on Tuesday evening.
He has been bailed to appear at Bromley Magistrates Court at 10:00 GMT on 27th February.
In a statement on their official website, Millwall said that Scanlon was not a season ticket holder or supporters club member at the club.
The development comes two days after Sky Sports News broadcast a Special Report on racism in football that appeared to show striker El Hadji Diouf being abused at The Den during a game on 18 November.
Both the Metropolitan Police and the Football Association requested a copy of Monday's programme to conduct their own investigations.