Scharner joined Wigan for the second half of the 2005–06 season. In his first match for Wigan, Scharner scored the winning goal against Arsenal in the League Cup at the JJB Stadium. He went on to start in the final for Wigan that season, a 4–0 defeat to Manchester United. He scored his first Premier League goal in the 24th round in a 1–1 draw with Everton. He quickly emerged as a starter, playing all games from the 22nd round onwards, scoring three goals while receiving five yellow cards.