To further develop his skills and to give him more minutes, Scharner was loaned to then-Austria affiliate club SG Untersiebenbrunn in the Erste Liga from July to October 2001, where he scored five goals in 16 league matches and also played in the ÖFB-Cup. He returned to his club in November and started getting minutes by the end of the month, playing against Rapid Wien, SV Salzburg and FC Kärnten. In the second half of the season he developed himself as a starter, seeing the kick-off in twelve of his 13 games, while seeing four yellow cards that season. He made his first goal for Austria Wien in a professional competition, opening the scoring in a Bundesliga match against Sturm Graz on 30 March. His strong away round also brought him into the Austrian national football team, debuting in a 0:0 against Cameroon on 17 April 2002.
Scharner debuted for the Austrian national football team in a 0:0 against Cameroon on 17 April 2002. He played the qualification round for the 2006 FIFA World Cup but Austria failed to qualify. Scharner retired in August 2006 after a 2-1 defeat to Hungary, criticising "unprofessional structures" within the ÖFB. Coach Josef Hickersberger banned him from the team and stated that he will never play for Austria as long as he manages it. He tried to make a comeback in 2008, when Austria co-hosted the 2008 UEFA European Championship but Hickersberger remained hard, not picking him. After Hickersberger was replaced, his successor Karel Brückner started nominating him again after the tournament and he was even promoted to team captain from 2009 to 2010. After then-coach Dietmar Constantini was fired, he tried to become player-coach but this was rejected. In August 2012 he was banned from the team permanently after leaving the team hotel when coach Marcel Koller refused to give him a leading role in the upcoming 2014 FIFA World Cup qualification. The chairmanship of the ÖFB has stated that he will never play for Austria again, no matter who coaches it. He played a total of 40 matches, scoring no goals.