Scott started his career in the youth system at Division One side Wimbledon under Geoff Taylor, but was released before making a first team appearance and joined non-league Sutton United. Scott was signed by Sheffield United for £50,000 in 1992, linking up with Geoff Taylor again, who was then the club's assistant manager. After loan spells at Bury and Chesterfield he signed for Brentford for £75,000 in November 1997, again linking up with Geoff Taylor, then Brentford's Director of Youth Football. He played 143 games for The Bees in all competitions during a five-year spell at Griffin Park. Scott moved on to Oxford United, again for £75,000, in January 2001. Scott moved to Leyton Orient in 2004, but was forced into retirement at the end of the 2004–05 season after a heart defect was discovered.
After his retirement, Scott landed a coaching role at Leyton Orient. He went on to become youth team manager. On 9 May 2007, Scott was appointed assistant manager at Brentford to Terry Butcher. On 11 December, Scott was named caretaker manager of Brentford following the sacking of Butcher. His caretaker spell was a successful one, and he landed the role permanently on 4 January 2008, signing a five-year contract.
His first calendar year in charge was recognised with an award, the BBC London "Manager of The Year" for 2008.
In his first full season in charge, Scott led the west London club to the 2008–09 Football League Two title (English football's 4th tier), confirming the championship with a 3–1 away win at Darlington on 25 April.
Scott was awarded the League Two Manager of the Month award for April/May 2009; which recognised his team's title and also the circumstances in which it had been achieved—four first choice strikers were hospitalised in the last 8 games of the campaign.
Scott was runner up of the LMA Manager of the Year Award for League Two in 2009 after the promotion winning season, losing out to Paul Tisdale of Exeter City. On 3 February 2011, he was sacked as manager of Brentford after a 4–1 defeat to Dagenham & Redbridge. His sacking was criticised by Wojciech Szczęsny when he posted Twitter tweeting "“What a joke! Andy Scott sacked?! He is a fantastic manager and Brentford will pay the price. They were struggling in League Two when AS took over! He is the only reason why Brentford is in League One.” Scott signed Szczęsny in 2009 and gave him more playing time.
On 13 April 2011, Scott was named manager of Rotherham United on a three-year contract. Scott was awarded the League Two Manager of the Month award for August 2011 after a good run of results and start with Rotherham. In March 2012 he was sacked after less than one year in charge.
On 22 February 2013, Scott was named manager of Aldershot Town following Dean Holdsworth's departure.
Almost two years later, on 21 January 2015, Scott was relieved of his duties along with his assistant Terry Bullivant.
On 1 July 2016, Scott returned to Brentford, this time as chief scout. later to be made Head of Recruitment after a re-structuring of the department.
He has been responsible for signing loan players from other Championship and Premier league clubs, most noatbly giving Wojciech Szczesny his league debut in 2010, Jordan Rhodes from Ipswich Town, Ryan Dickson from Plymouth (later sold to Southampton) & Tommy Smith (to be capped by New Zealand).
He is the brother of Rob Scott. He attended Wilson's School in Wallington. He studied Sports Studies at university.
BrentfordFootball League Two: 2008–09