In his final season for Wigan, he played in all 38 league games, scoring four goals while receiving six yellow cards. Wigan lost to Blackpool in the second round of the League Cup and to Notts County in the fourth round of the FA Cup. On 30 August 2009, he scored his first goal of the season against Everton. After a 5–0 defeat to Manchester United, Wigan manager Roberto Martínez preferred to use Scharner in an attacking midfield role. Scharner was a part of the team in November 2009 that suffered a historical 9–1 loss at the hands of Tottenham, scoring Wigan's only goal in the fixture although, when controlling the ball prior to shooting, he appeared to handle it. On 19 April 2010, he announced his decision to leave Wigan Athletic at the end of the 2009–10 season.