He was appointed vice captain in 1999. In 2001 he was once again forced out with re-occurring hamstring injuries, and was limited to eight games. Collingwood made the Grand Final in 2002 and Burns played a magnificent season, coming runner-up in the best and fairest once again. As a veteran of the club, he was only experiencing his first final when he played against Port Adelaide. He had 505 disposals for the season and was a dominant midfielder and forward, kicking twenty eight goals in the season. In 2003 he came third in the best and fairest. Injuries once again got hold of Burns in 2004 but he still managed to play nineteen games. He played every game in the 2005 season.
In March 2008, Scott Burns was appointed Collingwood captain for the 2008 season, replacing Nathan Buckley.
On 22 September 2008 Burns announced his retirement from AFL due to injury problems. He played a total of 265 games kicking 149 goals in his 14-year career.
He was appointed to be an assistant coach of the West Coast Eagles on 4 October 2008.