Leyton Orient After retiring from football in April 2005, Scott began coaching the Leyton Orient youth team, replacing
Dean Smith, who moved up to assistant manager. He remained in the role until his departure at the end of the
2006–07 season. Following a poor run of results and with a relegation into non-League football a possibility, Butcher was sacked on 11 December 2007 and Scott was named
caretaker manager. After three wins, one draw and one loss from his opening five games, Scott was named as the club's permanent manager on 4 January 2008. Seven wins and two draws from a 9-match spell between late December 2007 and mid-February 2008 raised the Bees to 11th position, but hopes of a
playoff finish were thwarted by a run of just four wins from the final 15 matches of the season. Scott signed a new five-year contract during the 2008 off-season and an overhaul of the squad and the shrewd loan signings of
goalkeeper Ben Hamer, The title win made Scott the first person to win a league championship as both a player and manager of Brentford.
2009–2011 Scott again overhauled the squad for the
2009–10 season in
League One and he again showed prowess in the loan market, signing young
Arsenal goalkeeper
Wojciech Szczęsny, up-and-coming teenage attacker
John Bostock and future stalwart
Toumani Diagouraga. Just six defeats between early December and the end of the season led to a strong 9th-place finish. Scott's Brentford had a torrid start to the
2010–11 season and sat bottom of the table after just two wins from the opening 11 matches. The early months of the season were notable for a run to the fourth round of the
League Cup, which featured wins over
Championship club
Hull City and Premier League
Everton on
penalties at Griffin Park, before the run ended with a loss in a penalty shootout away to Premier League side
Birmingham City. Scott also guided Brentford to the Southern Area finals of the
Football League Trophy, but winless run in league matches in January 2011 saw Scott and his assistant
Terry Bullivant sacked two days after a 4–1 away defeat to
Dagenham & Redbridge on 1 February. In recognition of his achievements as a player and manager with Brentford, Scott was inducted into the club's
Hall of Fame in November 2024.
Rotherham United On 13 April 2011, Scott was named manager of League Two club
Rotherham United on a three-year contract. He immediately made wholesale changes to the squad and instigated changes to the youth setup and the training ground. Four wins and one draw during the opening month of the
2011–12 season led to him winning the August 2011 League Two Manager of the Month award. With the club in 11th position in the table, Scott was sacked on 19 March 2012.
Aldershot Town On 22 February 2013, Scott took over as manager of League Two club
Aldershot Town on a deal until the end of the
2012–13 season. Scott and his assistant Terry Bullivant were unable to save the Shots from relegation to the
Conference Premier and the subsequent entry into
administration. Despite Aldershot residing in the relegation places in October 2013, the pair signed new three-year contracts. but with the club six points above the relegation zone, Scott and Bullivant were sacked on 21 January 2015. In August 2022, Scott revealed that he would not return to football management and that he had been "in management for a reason and that was to develop players, organise teams and get everyone playing the way I wanted to play. Realistically, where I was going to go after Aldershot was scrambling around at that level, I didn't want to be a
journeyman manager applying for every job. Now I'm forging out a new career where I'm fortunate to be in the position I am in". == Backroom roles ==