Stockport County In July 1990, he joined
Stockport County as a manager for their youth team and took over as first-team manager from
Danny Bergara in March 1995. He took the team into the
First Division from an automatic promotion place in 1997. He also took the club to the semi-finals of the League Cup where they were narrowly defeated 2–1 on aggregate by
Middlesbrough despite an impressive win at the
Riverside Stadium. During the same cup run, Stockport also defeated
Sheffield United,
Blackburn Rovers,
Southampton and
West Ham United, all of whom were in higher divisions than the club at the time.
Southampton This promotion brought him to the attention of Southampton, who offered him a contract to manage their
Premier League team. His reign during the 1999–2000 season was rocked by his arrest on charges of
child abuse during his employment as a care worker in the late 1980s. The case put tremendous strain on Jones, who was forced to defend his case on
Merseyside whilst managing a team based over 200 miles away on the south coast. In January 2000, Southampton decided to suspend him on full pay until the case was resolved, with
Glenn Hoddle taking over his managerial duties. When the case eventually came to court, it was thrown out in its first week, with the judge recording a not guilty verdict and commenting that the case "should have never reached the trial stage". Jones's new-look team quickly made an impact, hitting the top of the league by late September, and remaining in the automatic promotion spots over the following months. He won the Division One
Manager of the Month Award in February 2002, On 9 March 2008, Jones led Cardiff to their first
FA Cup semi-final tie since 1927 after beating
Premier League side
Middlesbrough 2–0 in the quarter-finals. On 6 April, Cardiff City beat
Barnsley 1–0 at
Wembley to book an
FA Cup Final place against
Portsmouth. Cardiff City lost the final, played on 17 May 2008, with the only goal of the game being scored by
Nwankwo Kanu for Portsmouth after 37 minutes. The start of the 2008–09 season saw veterans
Jimmy Floyd Hasselbaink,
Robbie Fowler and
Trevor Sinclair released and the sales of some of the team's biggest assets in
Glenn Loovens and
Aaron Ramsey. Despite this, Jones brought in several new faces and by November Cardiff found themselves in a play-off spot, earning Jones the Championship manager of the month for October. However, after spending the majority of the season in a play-off position, the side missed out on the final day of the season after suffering a 1–0 defeat against
Sheffield Wednesday. Despite missing out on the play-offs, Jones had led Cardiff to their highest league position for 38 years. The start of the 2009–10 season saw Cardiff in top form, beating
Scunthorpe United 4–0 putting them top. In the first five games, Cardiff were only in the top two until a 1–0 defeat against
Newcastle United which put Cardiff eighth. On 7 November 2009, Jones earned the Championship Manager of the Month for October, the same day Cardiff lost the first
South Wales derby 3–2 at
Liberty Stadium. At the end of the season, Jones took Cardiff to their highest finish in the league in 39 years, fourth place, meaning they would take part in the play-offs. Cardiff beat Leicester at the
Walkers Stadium 1–0, thanks to
Peter Whittingham's free kick but lost the second leg 3–2, resulting in extra time. The match eventually went to penalties with Cardiff winning 4–3. In the
Play-off Final at Wembley, Cardiff suffered a 3–2 defeat to
Blackpool. In the 2010–11 season, Cardiff started the season with four wins out of five games. By the end of October, Cardiff had only lost two games and Jones received the October Championship Manager of the Month, whilst leading scorer
Jay Bothroyd won Player of the Month. The club suffered a big loss of form in November and December, with only two wins out of nine games. They finished the season in fourth place behind rivals
Swansea City. Cardiff then faced fifth placed
Reading in the play-off semi-final, where they lost 3–0 on aggregate. Jones was later sacked from Cardiff City on 30 May 2011.
Sheffield Wednesday Jones was appointed
Sheffield Wednesday boss on 1 March 2012, replacing
Gary Megson who was sacked the day before. His first official game in charge was against
Bury and Wednesday came out 4–1 winners, the following game ended with a 3–0 win after three goals in the first ten minutes. After leading Wednesday to five wins and a draw during his first month in charge, Jones was awarded
League One Manager of the Month for March 2012. Jones then led Wednesday to another five wins and a draw during his second month in charge and was awarded the Manager of the Month award for April 2012. On 5 May 2012, Jones led Wednesday to promotion from Football League One to the Championship after beating
Wycombe Wanderers 2–0. Jones' first game in charge of Sheffield Wednesday in the Championship was a 2–2 draw away to
Derby on 18 August 2012. Two home wins in the next two matches and a
League Cup victory over
Premier League side
Fulham saw Jones stretch his unbeaten start as Sheffield Wednesday manager to eighteen matches. Jones' first defeat eventually came on 1 September 2012 after eighteen games unbeaten, a 2–1 loss away to
Crystal Palace. Jones returned to his former side Cardiff for the first time as Sheffield Wednesday manager on 2 December 2012, losing 1–0. In February 2013, Jones was fined £2,000 and given a one-match touchline ban by the
FA for misconduct after a fracas on the touchline with
Brighton & Hove Albion coach
Charlie Oatway during Wednesday's 3–1 victory over Brighton. Jones later said that he disagreed with his fine and described Oatway as a "nobody". Jones was dismissed on 1 December 2013, with the club second from bottom in the Championship, having won only one league match all season.
Hartlepool United On 18 January 2017, Jones returned to football management when he joined
Hartlepool United of League Two. Jones joined with the North-East club 19th in the table and four points clear of the relegation zone. Hartlepool's form deteriorated further, winning only 13 points from a potential 51, and left the club by mutual consent on 24 April 2017. During Jones' last match in charge of Hartlepool, club president
Jeff Stelling urged him to quit, in an impassioned speech on
Soccer Saturday, following a home defeat to
Barnet which had placed Hartlepool in the bottom two. Notified of this public criticism afterwards, Jones told reporters that Stelling showed a "lack of respect" and accused him of being "hypocritical", having been in his office when Hartlepool had gone five games without a loss. Upon Jones' departure, Hartlepool striker
Billy Paynter criticised the manager's tactics. Despite Hartlepool winning their final game of the season against
Doncaster Rovers, a late goal from Newport consigned Pools to relegation from the Football League for the first time after joining in 1921.
Post-Hartlepool In April 2018, Jones applied for the role of head coach of the
Singapore national team but was unsuccessful. Jones began working as a consultant at
Bury in July 2019. His first task with the club was helping them to appoint
Paul Wilkinson as manager. Jones left Bury following the club's expulsion from the Football League in August 2019. ==Acquittal of child abuse==