Duff helped Blackburn achieve promotion back to the Premier League in 2001 and then win the League Cup in 2002, beating Tottenham Hotspur 2–1 at the Millennium Stadium. Following the 2002 World Cup, Duff signed a new four-year contract with Rovers. Despite injury problems in the 2002–03 season, he finished as Blackburn's top goalscorer with 11 goals, which helped his team finish sixth and qualify for the UEFA Cup.