In 2001, 29-year-old Ferguson was linked with the management post at Wrexham, following the departure of
Brian Flynn. At the time, he assisted caretaker manager
Joey Jones. After manager
Denis Smith was sacked in January 2007, Ferguson was again touted as a candidate, having by now played well over 300 games for the club, but coach
Brian Carey was appointed instead. There were suggestions that Ferguson and Carey had clashed, as Ferguson had expected to be appointed. Carey, who had left Ferguson on the substitutes bench for his first game, denied this. The pair had argued a year previously, following a defeat to
Leyton Orient. Ferguson later stated he was disappointed not to be considered for the management position, and stated the club would have done better under him than they did under Carey.
Peterborough United Shortly after his father celebrated 20 years as manager of
Manchester United, Ferguson followed him into football management. In January 2007 he left Wrexham to become player-manager of fellow
League Two side
Peterborough United. Previous manager
Keith Alexander had been sacked after a run of six straight defeats. He led the club to a 10th-placed finish in his first season of management. In his first full season of management, he took Posh to second place in
League Two, gaining promotion. He was named League Two manager of the month for March 2008, after Peterborough won six games out of eight in the month. In his second full season, 2008–09, he led Posh go to second place and automatic promotion to the
Championship. He also won the League One Manager of the Month award for March 2009, following six straight wins. Ferguson left Peterborough in November 2009, by mutual consent, with the club bottom of the table.
Preston North End In January 2010, Ferguson signed as manager of
Preston North End. His first game at home as a manager was an FA Cup match against Chelsea on 23 January 2010 which his side lost 2–0. On 14 September 2010, Ferguson was charged with misconduct by the FA after his behaviour in the tunnel towards the referee after a 4–3 Championship defeat by Burnley. During a disappointing period as manager of Preston, in a spell which lasted less than a year, Ferguson had a comeback win in September 2010 when his Preston side beat Leeds United 6–4 after being 4–1 down at
Elland Road. After the match Ferguson said: "I have never been involved in such an amazing game." After 49 games in charge, winning 13, drawing 12 and losing 24 games, he was sacked as manager on 29 December 2010, with Preston North End bottom of the Championship. Following his sacking by Preston, his father Sir Alex Ferguson immediately recalled all three Manchester United players on loan at Preston;
Joshua King,
Ritchie De Laet, and
Matty James. In addition, the Stoke City manager
Tony Pulis recalled the two Stoke players on loan at Preston;
Danny Pugh and
Michael Tonge. This meant that in a single week, Preston had lost five key first-team players, effectively sealing the team's relegation.
Return to Peterborough United In January 2011,
Gary Johnson left his job as manager at Peterborough United, with the club several points adrift of the playoff places. On 12 January 2011, Ferguson was re-appointed as manager at Peterborough on a four-and-a-half-year contract. His first match ended up in a defeat away to league leaders
Brighton & Hove Albion, but the following week, in his first game at London Road since his return, Peterborough beat
Hartlepool United 4–0. The club ultimately finished fourth in League One, and after beating
Milton Keynes Dons 4–3 on aggregate, reached the
play-off final at
Old Trafford against
Huddersfield Town. Peterborough went on to defeat Huddersfield 3–0 to clinch a return to the
Championship, just one year after they had been relegated. By the end of the season, Peterborough had become the top-scoring side in the whole country, with 106 goals in total. Peterborough spent two seasons in the Championship after winning promotion, before being relegated back to
League One after losing to
Crystal Palace 3–2 on the final day of the season. Peterborough had led the match with seven minutes remaining, but went on to lose in the final minute; a draw would have been enough to keep Peterborough in the Championship. Their total of 54 points during that season is to date the highest amount accrued by a relegated side in Championship history. On 21 February 2015, following a 3–0 away defeat at
Milton Keynes Dons which left the team 15th in the League One table, Ferguson left Peterborough United by mutual consent.
Doncaster Rovers Ferguson was appointed manager of League One club
Doncaster Rovers on 16 October 2015. They were relegated at the end of the 2015–16 season, but a third-place finish in their only season in
League Two saw the club win promotion back to League One in May 2017. Ferguson resigned from his role as manager on 4 June 2018, after guiding Rovers to 15th-placed finish in their first season back in League One.
Second return to Peterborough United Ferguson was appointed as manager of League One club Peterborough United on 26 January 2019 for the third time with a deal agreed until the end of season after the dismissal of
Steve Evans, with
Gavin Strachan as his assistant. In May 2021, after missing out on the previous season's play-offs due to the season being curtailed by the COVID-19 pandemic, Ferguson successfully guided Peterborough to promotion to the Championship. On 20 February 2022, the following day from a last-minute 1–0 defeat to relegation rivals
Derby County that left Peterborough in 23rd position, five points from safety, it was announced that Ferguson had resigned during a phone call to joint-owner
Darragh MacAnthony.
Third return to Peterborough United On 4 January 2023, after the dismissal of
Grant McCann with
Cliff Byrne as his assistant, Ferguson returned for his fourth stint as manager to Peterborough United on a contract until the end of the season with the club sitting in eighth position in League One. They ended in sixth, and a place in the play-offs. In the play-off semi-final, Peterborough were defeated on penalties by
Sheffield Wednesday despite winning the first leg 4–0. At the end of the
2022–23 season, Ferguson signed a new three-year contract. In the league, Peterborough finished fourth but lost the League One play-off semi-final to
Oxford United. In the 2024–25 season, Peterborough failed to get promotion, but they became the first team to retain the EFL Trophy, beating
Birmingham City in the
final. On 25 October 2025, Ferguson was sacked following a 2–1 home defeat to
Blackpool that left
the Posh bottom of the league with just ten points from thirteen matches. ==Personal life==