He started his coaching career at Leyton Orient as joint manager with John Sitton shortly before the end of the 1993-94 season. The duo continued through a very difficult 1994-95 season, which ended with the club finishing bottom of the Second Division and being relegated, and Turner and Sitton left with three games remaining after new chairman Barry Hearn informed them that they would be replaced for the following season. Turner subsequently recounted that although he was officially joint-manager, in reality his role was more akin to being the assistant manager to Sitton.
Following his departure from Orient, Turner was appointed the reserve team coach at Leicester City by manager Mark McGhee and later moved with McGhee to Wolves, where he was appointed youth team coach.
His first solo managerial position came at Hartlepool United in 1999. Turner took over when Hartlepool were bottom of the Football League, saved them from relegation and turned them into promotion contenders. They gained promotion at the end of the 2002–03 season but Turner had moved back to his old club Sheffield Wednesday six months before the success was achieved under his successor Mike Newell.
Turner was appointed Wednesday manager in November 2002. He faced with the difficult task of saving Wednesday from sliding into the third tier of the league for the first time in a quarter of a century. The Owls improved during the final stages of the season, achieving some strong results, but a 1–1 draw with fellow strugglers Brighton (who lost their fight to stay up on the final day) condemned them to relegation. Turner was optimistic of getting the Owls back into the Premiership by 2008, but their Division Two campaign in 2003–04 was dismal. They finished 16th in the table (their worst position for nearly 30 years) and were the division's lowest scorers with 48 goals. However, the side had been hampered by a significant injury list and this had contributed to their poor league form. In the summer of 2004, Chris Turner was given £500,000 to spend in the transfer market and built a team which ultimately won promotion at the end of the following season. However, Turner was controversially sacked in September 2004 after a slow start to the League One campaign leaving Wednesday languishing in 14th place.
Chris Turner returned to management with another financially insecure club, Stockport County, soon after being dismissed by debt-ridden Wednesday. County were bottom of League One at the time and survival proved too great a task for both the playing squad and Turner, and Stockport were relegated to League Two long before the end of the season. Despite a takeover by a Supporters' Trust and some promising signings, County struggled to find form in the early part of the 2005–06 season. By the end of November, Stockport had drawn eleven of their nineteen league games and won just two. December saw County in crisis, with a run of four consecutive defeats in the league, culminating in a humiliating 6–0 defeat by local rivals Macclesfield Town on Boxing Day. With Stockport now five points adrift at the bottom of the league, Chris Turner left the club by mutual consent on 27 December 2005. Following Turner's departure, former Stockport player Jim Gannon took over as manager and oversaw a remarkable recovery which saw County retain their league status in a nail-biting finish to the season.
In February 2006, Turner returned to Hartlepool United in the newly created position of Director of Sport. In December 2008, Turner took over as caretaker manager at Hartlepool following the departure of Danny Wilson, in addition to his Director of Sport role at the club.
On 19 August 2010, Turner left his role as caretaker manager and director of sport of Hartlepool United with immediate effect, sparking shock around the club. Russ Green sooned followed Turner out of the Victoria Park door. On Thursday 14 October 2010, Turner confirmed the rumours that he was indeed part of a bid to buy his boyhood team Sheffield Wednesday in a £15 million deal. The consortium that Turner was a part of ultimately did not make a successful bid for the club however, and the club was instead purchased by Milan Mandarić in December 2010.
Turner became chief executive of Chesterfield F.C. on December 21, 2011, replacing Carol Wilby.