He also played in the Football League for Wigan Athletic, Norwich City, Wolverhampton Wanderers, Tranmere Rovers, Stockport County and Burnley.

Following his departure from Wigan Athletic, Cook remained unemployed until March 2021 where he was appointed as the manager of Ipswich Town on a contract until 2023.

After a falling out with Burnley manager Stan Ternent, Cook went on loan to his former club Wigan Athletic, but made just six appearances before he was re-called to again take his place in the starting line up at Turf Moor.

Cook signed for non-league side Accrington Stanley and went on to become a first team regular in their push for promotion to the Football League.

The testimonial was played on 2 May 2006 at the Interlink Express (now the Wham) Stadium; Accrington against a Burnley Select XI featuring old teammates Dean West, Lenny Johnrose, Ian Cox, Kevin Ball and Cook's son Liam.

Cook was appointed manager of Conference side Southport on 13 June 2006,[5] a post he was sacked from in January 2007 following defeat at Northwich Victoria.

On 27 April 2007, Cook was appointed manager of Sligo Rovers taking over from Rob McDonald, who resigned before the start of the season.

[9] He led the team to finish 14th in League Two at the end of the 2011/12 season and continued to manage the side for the opening months of the following campaign.

On 25 October 2012, Cook joined League Two rivals Chesterfield on a two-and-a-half-year contract, taking over from Tommy Wright, who had been in charge of the Derbyshire club on a caretaker basis following the departure of John Sheridan.

[13] On 31 May 2017, Cook was appointed manager of newly relegated League One club Wigan Athletic on a three-year contract, after a compensation package was agreed with Portsmouth.

[14] He led Wigan to the League One title and on an impressive FA Cup run that claimed three shocks against top flight opponents West Ham United, AFC Bournemouth and Manchester City.

[15] Cook resigned as Wigan manager on 29 July 2020, following the club's relegation from the Championship due to a 12-point deduction after the Latics entered administration.

[18][19] On 7 April 2021, Ipswich Town was taken over by US investment group Gamechanger 20 Limited, with the club confirming that Cook would remain as manager under the new ownership.

[21] Ahead of the 2021–22 season, Cook oversaw a major turnover in both the playing squad and coaching staff, backed by the club's new US owners.

[22] Despite these changes and many tipping the club for promotion, Ipswich made a poor start to the season, taking only two wins in their opening 10 matches.

[26] He won the award for a second time for January 2024 having overseen five victories from five matches as his side sat over twenty points clear at the top of the table.