After four senior Bundesliga appearances in the 2012–13 season with Hamburg, Scharner was signed on loan by former club Wigan Athletic, on transfer deadline day. He helped the club to reach the FA Cup final after they beat Millwall 2–0 at Wembley. Scharner said it was his "best moment in football". On 11 May 2013 Scharner won the FA Cup with Wigan, playing the whole game in a 1–0 upset win against Manchester City. Only three days later, Wigan were relegated from the Premier League following a 4–1 defeat against Arsenal.