He joined Wigan Athletic in December 2001 for £600,000. Prior to the start of Wigan's debut season in the Premier League he had missed only one match for the club but was injured at the start of the 2005–06 season with Wigan's new signing Mike Pollitt taking his place in the side. Filan, however signed a new contract which kept him at the club until 2007. Seeing out his contract with Wigan, he was released at the end of the season. Whilst at Wigan he appeared as a substitute in the 2006 Football League Cup Final when Pollitt had to come off early in the first half with an injury. He is also remembered for saving a Nolberto Solano penalty in a 1–0 win over Newcastle United in February 2007.