As chairman from 1997, Paphitis took Millwall out of administration and on to the 2004 FA Cup Final at the Millennium Stadium. He is perhaps best known for his work to reduce football hooliganism, and appointing as Millwall manager Dennis Wise, and together they guided the club to their first official appearance in the final of the FA Cup and European football. After almost eight years at the helm of Millwall, Paphitis stepped down from his role as chairman in 2005.