Leicester City manager

After the sacking of Leicester manager Craig Levein, following 18 months in charge, Kelly stepped up from his assistant manager role to take control on a caretaker basis.

In his first ten games in charge his team took 21 points from a possible 30, steering the side up the Championship table and away from the threat of relegation to League One. He was awarded the Championship Manager of the Month award for March 2006. This followed wins over relegation rivals Hull City and Millwall, as well as victory against Luton Town and a creditable draw against Premiership-bound Reading. In recognition of his achievements, on 14 April 2006 he signed a one-year rolling contract, confirming his status as manager.

On 11 April 2007 Kelly was sacked due to a poor run of results, his final game being a 3–0 defeat away to Plymouth Argyle. He was replaced by Nigel Worthington until the end of the season.

Preston North End

In May 2007 he joined Preston North End as part of the club's coaching staff.^[2] After the sacking of manager Paul Simpson.^[3] The club appointed Alan Irvine as the Club's new manager on 20 November 2007, with Kelly his assistant. In the season 2008/2009, Preston with Irvine and Kelly reached the Championship Play-Off's. Narrowly missing out on a place in the final, losing 2-1 on aggregate to Sheffield United.

Kelly acted as caretaker manager following the departure of Alan Irvine in December 2009, a 7–0 FA Cup win over Colchester being his only game in charge. He left the club following the appointment of Darren Ferguson as manager.

Sheffield Wednesday

Kelly re-united with Alan Irvine at Sheffield Wednesday, once more as assistant manager. After Irvine left the Owls in February 2011,^[4] Kelly also departed after Gary Megson was appointed as manager and made changes to the coaching staff.^[5]

Nottingham Forest

Kelly joined Nottingham Forest as assistant manager to Steve McClaren's backroom team in the summer of 2011, with Jimmy Floyd Hasselbaink the club's First Team Coach. When McClaren resigned on 2 October after a dispute with the club's board, Steve Cotterill was appointed the club's new manager on 14 October with Kelly remaining as Forest's assistant manager.^[6]

He was placed 'temporarily in charge of first team affairs' during the pre season of the 2012/13 campaign after the sacking of Steve Cotterill by the club's new owners.^[6] Following the subsequent appointment of Sean O'Driscoll,^[7] Kelly again reverted to the role of assistant manager.

He remained assistant manager when O'Driscoll was in turn sacked in December 2012 and replaced by Alex McLeish, only to find himself as caretaker manager yet again just six weeks later when McLeish resigned. Billy Davies was announced as the club's new manager on 7 February, though it was also announced that Kelly would remain in his role at the club.

West Brom

During the summer of 2014, Alan Irvine was appointed the manager of West Brom, again hiring Kelly as his assistant manager. On 29 December 2014, Kelly took over the team alongside coaches Keith Downing and Dean Kiely after Irvine's dismissal.^[8] on 1 January 2015, they drew 1–1 away at West Ham United.^[9] and then recorded a 7–0 victory against Gateshead in the FA Cup on 3 January 2015, following the appointment of Tony Pulis as Head Coach.

On 5 January, Kelly, Kiely and Downing all departed the club, with Pulis wanting to reshape his own backroom team.^[10]

Return to assistant

On 3 June 2015, he was appointed as Assistant Head Coach to Uwe Rosler at Leeds United.^[11] In December 2015, Kelly agreed to become first team coach and link up again with Alan Irvine alongside Paul Lambert at Blackburn Rovers. After they successfully guided the club to Championship safety, all three coaches left Rovers in the summer of 2016 before the start of the following season.

Kelly once again joined up with Rösler at Fleetwood Town in 2016 and left in the summer of 2018. Kelly was appointed assistant manager to Ryan Lowe at Football League Two side Bury on 10 July 2018, as the club targeted an immediate return to League One.^[12]

On 1 January 2019 Kelly was announced as assistant coach to Rösler at Sweden's Malmö FF. On 7 February 2020 he followed Rösler to Fortuna Düsseldorf.

Barrow

On 4 September 2020 Kelly was appointed as assistant manager to David Dunn at League Two side Barrow.^[13] Following the sacking of Dunn on 13 December, he was appointed as caretaker manager,^[14] leading the club to victories over Cheltenham Town and Port Vale.^[15] With the appointment of new manager Michael Jolley, he returned to his role as assistant manager for Barrow's game with Tranmere Rovers on 29 December.^[16]

On 21 February 2021, Barrow parted company with Jolley and Kelly was once again named as caretaker manager, this time until the end of the season.^[17] During his second stint as caretaker manager, he presided over an upturn of form and on 27 April, with two matches remaining, Barrow secured their Football League status for the following season with a 2–0 win at Forest Green Rovers.^[18] He turned down the job on a permanent basis^[19] and on 26 May he left the club.^[20]

Wigan Athletic

On 25 June 2021, Kelly joined Wigan Athletic as assistant manager.^[21]

Return to Preston North End

On 18 July 2023, Kelly joined Preston North End as a first team coach, returning to the club and reuniting with manager Ryan Lowe, who he worked with previously at Bury.^[22]