Burgoyne made his AFL debut in 2002. He had been a steady contributor across the forward line for the Power, before becoming a rebounding defender to great effect.
After a series of midfield performances that culminated with selection to the All Australian Team in 2006, he was described by retiring Port player Josh Francou as being "as good as Judd".
Burgoyne was important in The Power’s midfield in 2008, despite attracting the opposition’s best tagger most weeks. While not reaching the heights of past seasons, he finished fourth in the best and fairest and was second at the club in centre clearances, tackles and inside 50s, and fourth in goals (23), contested possessions and bounces. 2009 was a disappointing year after injuring his knee in round three and missing three months of footy. He was able to come back and play a few good games late in the year.
As Vice-captain he shocked the football club by requesting to play for a Victorian team in 2010 after his brother had retired. Port traded him to Hawthorn in a complicated deal involving four clubs, with Essendon and Geelong also involved. He was allocated former club champion Shane Crawford's No. 9 jumper.
After having surgery on his knee during the off season that delayed his preparation for the 2010 season, Burgoyne suffered a broken jaw while playing for Box Hill. He made his debut against Richmond in Round 8, 2010. Burgoyne played the last sixteen games of the season.
During 2011 Shaun Burgoyne played excellent football for Hawthorn, showcasing his silky disposal and hard running. He was part of a side that was unlucky to lose a preliminary final to eventual runners up Collingwood by 3 points.
Burgoyne was part of Hawthorn's losing side in the 2012 AFL Grand Final.
In 2013, Burgoyne's performance in the Preliminary Final against Geelong saw him kick 3 goals and also provide goals assists, with his final goal putting Hawthorn back in front late in the 4th quarter. The match ended the 11-game losing streak against Geelong, in effect since the 2008 Grand Final win.
On 28 September 2013 Burgoyne became a dual Premiership player after Hawthorn defeated Fremantle Football Club in the Grand Final in front of 100,007 fans at the M.C.G. Burgoyne was the only player to remain completely in his game outfit when the players were presented on stage following the conclusion of the post-match concert.