Born in Bolton, Lancashire, Flitcroft began his career as an apprentice with Preston North End, who he signed professional forms with in May 1992. He was to spend the following season briefly involved in the first-team at Deepdale, but after a loan spell with Lincoln City, he was allowed to join Chester City in December 1993. Flitcroft was to make eight appearances as Chester pipped Preston to promotion from Division Three. Apart from some long spells out injured, Flitcroft was a regular in the Chester midfield until the end of the 1998–99 season when he rejected a new contract and joined Rochdale. In four years at Spotland, Flitcroft helped Rochdale qualify for the Division Three play-offs in 2001–02 and reach the FA Cup fifth round the following season. He switched to Macclesfield Town in July 2003 before moving on again, to fellow north-west side Bury just six months later. He was to spend three years as a regular with the Shakers, making exactly 100 league appearances until he joined non-leaguers Hyde United. But Flitcroft returned to Rochdale as assistant manager to Keith Hill midway through the 2006–07 season. Towards the end of the 2008–09 season Flitcroft came on as substitute in the last scheduled game of the season at home to fellow play-off rivals Gillingham. The following season, he started a Football League Trophy game against Bradford City in what proved to be his final match as a professional.
Coaching career
After retiring as a player, Flitcroft joined the coaching staff at Rochdale. On 1 June 2011, Flitcroft was appointed assistant manager at Barnsley after following manager Keith Hill to Oakwell. He was made caretaker manager of Barnsley after Hill was sacked during the 2012–13 season. After two wins in three games as caretaker manager, Flitcroft was appointed to the position. Flitcroft guided the club to Championship safety on the final game of the 2012–2013 season, following an impressive set of results in 2013 and a 2–2 away draw at Huddersfield Town. He signed a rolling contract on 9 May 2013 to keep him at the club, alongside assistants Martin Scott and Micky Mellon. On 30 November 2013 Flitcroft was sacked by Barnsley after a 3–0 home defeat by Birmingham City.
Bury F.C
Flitcroft was officially announced as the manager of Bury on 9 December 2013. Flitcroft took the club from the face of relegation to a 12th-place finish in the top half of the table including a 1–4 win at Mansfield Town and a 4–0 win against Plymouth Argyle. During the next season, Flitcroft led Bury to promotion back to League One with a 1–0 win over Tranmere Rovers on the final day of the season. On 16 November 2016, Flitcroft was sacked after a run of 11 games without a win.
Swindon Town F.C
On 5 June 2017, Flitcroft was appointed as manager of Swindon Town,. Flitcroft guided the Robins to seventh before taking up the managers vacancy at fellow League Two contenders Mansfield Town on 1 March 2018.
Mansfield Town F.C
Flitcroft was announced as Mansfield Town manager on 1 March 2018 following the resignation of Steve Evans. Flitcroft presided over a poor run of form with the Stags gaining only two wins in twelve, ultimately leading them to three points outside the League Two playoffs in eighth place. At the end of the season, amongst pressure from fans, Flitcroft promised to build a 'promotion winning squad' leading to the addition of six new players. By the end of December Mansfield Town had only lost once under Flitcroft in the 2018/19 season. They were additionally the only side in the top four English divisions unbeaten away from home, until a 2–1 loss against Carlisle. Flitcroft's contract was terminated by Mansfield Town on 14 May 2019 together with assistant Ben Futcher after failing to achieve promotion to League One, having lost to Newport County in the play-off semi-final.
On 31 August 2019, Flitcroft was named Assistant Manager at his home town team, Bolton Wanderers, as assistant to new Bolton manager Keith Hill, the duo working together once again after spells together at both Rochdale and Barnsley. On 12 June 2020 it was announced that Bolton Wanderers would not be renewing his contract after relegation to League Two.