Scharner started his professional career with Austrian Bundesliga sides Austria Wien and SV Salzburg, before moving to Norwegian Tippeligaen in late 2004, starting for SK Brann. In January 2006, he entered the Premier League where he played for over six years, playing for Wigan Athletic and West Bromwich Albion, respectively. After a short time as a free agent, he transferred to Bundesliga veteran club Hamburger SV in August 2012, before returning to Wigan Athletic on loan in January 2013 - winning the FA Cup. He announced his retirement, at age 33, in September 2013.