Kirk played 241 games for the Swans since making his debut in 1999, including the final 200 without missing a match. He was nominated All-Australian in 2004. Kirk won the best and fairest twice, in 2005, the year the club won the AFL premiership, and again in 2007. He was co-captain of the Swans from 2005–2010.

Kirk made his debut in Round 19 of the 1999 season against the North Melbourne Kangaroos and recorded 19 disposals and kicked 3 goals, he played a total of 12 games in his first two seasons but broke into the side in 2001, to play 19 games and kick 14 goals and, he went onto play 18 games in 2002 and in 2003 had a break out year, in which Kirk played all of Sydney’s 24 games and recording 140 tackles, and became an integral part of the engine room at the Swans. Kirk also represented Australia in International Rules against Ireland

In 2004, Kirk took his game to another level, playing all 24 games, his season was highlighted with a 33 disposal and 7 tackle effort in a Round 15 victory over the Adelaide Crows, as well as a 30 disposal, 6 tackle and 1 goal effort in their Round 19 loss against the Kangaroos. He was rewarded with his excellent season with selection in the 2004 All-Australian team, in which he was selected on the interchange bench. Kirk also represented Australia in International rules football against Ireland.

In 2005, Kirk became a Co-Captain of the Swans, alongside Barry Hall and Leo Barry, and played all 26 games for the Swans, highlighted with a 31 disposal 8 tackle performance against the Essendon Bombers in a Round 7 win, and a 29 disposal, 7 tackle and 1 goal effort in the Swan’s Round 16 win over the Melbourne Demons. Kirk became a premiership player when the Swans defeated the West Coast Eagles by 4 points in the 2005 AFL Grand Final. He was rewarded with his first Bob Skilton Medal, as Sydney’s best and fairest, in a season in which he recorded 570 disposals and laid 136 tackles, including 22 disposals and 7 tackles in their drought breaking premiership victory.

2006 saw Kirk play all 25 games and recording 142 tackles. He recorded 10 tackles in their Round 9 win over the Hawthorn Hawks and 11 tackles in their loss over the West Coast Eagles in their Round 15 grand final rematch. He performed strongly all season, and the Swans again matched up against the Eagles in the 2006 AFL grand final , in which Kirk recorded 27 disposals and laid 9 tackles. The Swans eventually lost the decider by 1 point. Kirk won the Robert Rose Award at the 2006 AFL Players Association awards, for being voted the most courageous player in the league.

The 2007 AFL season saw the Swans win 12 games and eventually bow out in the Elimination final against the Collingwood Magpies, Kirk played 23 games and laid 149 tackles, and had 10 or more tackles 4 times, highlighted with 13 tackles against Richmond in round 2. He also recorded 516 disposals for the season. He was rewarded with his second Bob Skilton Medal, as Sydney’s best and fairest at the conclusion of the 2007 season.

In 2008, Kirk was given the honour of meeting with the Dalai Lama during his Australian tour in which he presented the Dalai Lama with a signed Swans guernsey. Kirk is known as a practicing Buddhist and has a tattoo of a Buddhist symbol on his back. When the young Swan Dan Hannebery seemed anxious, Kirk recommended that he do some meditation and read The Power of Now and A New Earth by Eckhart Tolle.

The 2009 AFL season saw the Swans have a somewhat disappointing season, only managing 8 wins for the season, Kirk performed consistently as always and recorded his career best of 170 tackles and recorded 14 tackles in their Round 19 win over Richmond. Kirk also racked up 468 disposals, and recorded 33 disposals against the Port Adelaide Power in Round 9.

2010 was Brett Kirk’s last season in the AFL, he recorded 397 disposals and laid 117 tackles and played his final game in the Swans Semi final loss against the Western Bulldogs. He was rewarded with the AFLPA Best Captain Award and also the AFLPA Madden Medal.

In 2011, he spent six months travelling the world and spreading the word about football as the AFL’s International Ambassador.