Scott was picked by the Brisbane Bears in the 1993 AFL Draft with the 12th draft pick and moved to Queensland while still studying at St Kevin's College. He studied at Brisbane Boys' College during his first years as an AFL player.
Scott made his AFL debut in 1994 with the Brisbane Bears, taking out the Norwich Rising Star award.
Scott became one of the AFL's toughest defensive players, using his strength to outmuscle opposing forwards. Along with his brother Brad, they were nicknamed the Kray brothers by some fans for their forceful and ruthless styles of play.
During Brisbane's three-peat era Scott was part of a powerful backline also containing Mal Michael, Chris Johnson and Justin Leppitsch. He caused controversy in round 1 of 2005, when along with Mal Michael he crashed into St Kilda's Nick Riewoldt after Riewoldt chose to stay on the ground with a broken collarbone. In the same game Scott also had several teeth knocked out after receiving a back-handed fist from opponent Aaron Hamill.
After participating in 2 premiership sides, Scott's later career was plagued with injuries, but his occasional appearances showed his experience and skill. Brisbane's round 22 match against the Geelong Football Club on 1 September 2007 was his last after announcing his retirement. In 2008, Scott joined Fremantle as an assistant coach.
In 2010, Scott was a frontrunner for the Port Adelaide Football Club senior coaching position to replace the sacked Mark Williams but ultimately fell short and caretaker coach and former Port captain, Matthew Primus, was chosen by the selection committee to be the club's senior coach. The media speculated that Scott was considered the second best applicant by the selection committee. On 18 October 2010, it was officially announced by the Geelong Football Club that Scott would be their new coach, following Mark Thompson's resignation at the end of the 2010 season.
Scott had a brilliant start to his AFL coaching career, with Geelong winning its first thirteen matches of the 2011 season. His thirteen wins in succession was the best start to a coaching career in almost 80 years. But this streak was broken in Round 15, when the Cats went down to Essendon by four points.
Scott coached Geelong to its third Grand Final in five years, and became the first coach since Malcolm Blight in 1997 to win a premiership as a first-year club coach, when Geelong defeated Collingwood in the 2011 AFL Grand Final by 38 points. He is also the youngest premiership coach since Alex Jesaulenko in 1979 to win a Grand Final.
In August 2014, Scott signed a two-year contract extension extending his tenure as senior coach of Geelong until the end of 2017.Statistics are correct to the end of the 2016 season
TeamVFL/AFL Premiership (Brisbane Lions): 2001, 2002
IndividualMerrett-Murray Medal (Brisbane Lions): 1998
Brisbane Lions Vice-Captain: 1999-2004
Norwich Rising Star Award (later named the Ron Evans Medal): 1994
AFL Rising Star Nominee: 1994 (Round 7)
Brisbane Lions - Most Professional Player: 1999
Brisbane Lions Team of the Decade (2000-2010) - Half-Back Flank
TeamVFL/AFL Premiership (Geelong): 2011
IndividualJock McHale Medal: 2011
Australia Coach for International Rules Football: 2017
Scott's identical twin brother Brad Scott played alongside him at the Brisbane Lions and is now the coach of North Melbourne. He is three minutes older than Brad.