Cooper began his coaching career at Wrexham's academy while playing as a defender in the Welsh football leagues.

He moved to Liverpool in 2008 and was appointed manager of their academy in 2011. Cooper joined the England youth set-up in 2014, initially coaching the U16s, before winning the 2017 FIFA U-17 World Cup with the U17s.

[6] He was signed by manager Brian Flynn, who suggested Cooper pursue a coaching career instead of playing professionally.

[6] Cooper later played for Total Network Solutions (now called The New Saints), Rhyl, Bangor City and Porthmadog in the Welsh football leagues.

"[23] Cooper was appointed head coach of Championship club Swansea City on 13 June 2019 on a three-year contract.

[24] His first match was a 2–1 win against Hull City at the Liberty Stadium, with goals from Borja Bastón and Mike van der Hoorn.

[25] Cooper was named the EFL's Championship Manager of the Month for August after Swansea's unbeaten start to the season saw them move top of the league, with 16 points from 18.

[30] On the final day of the season, Swansea beat Reading 4–1 to finish sixth, moving into the play-offs ahead of Nottingham Forest on goal difference.

[41] On 29 May 2022, Cooper led Nottingham Forest to promotion to the Premier League, after a 1–0 win over Huddersfield Town in the Championship play-off final at Wembley Stadium.

[47] On 20 June 2024, Cooper was appointed as manager of newly promoted Premier League side Leicester City on a three-year contract.

[48] Following a winless run of five games, Cooper was sacked on 24 November, the day following an 1–2 home defeat against Chelsea while being managed by Enzo Maresca, the ex-manager of the Foxes.

[20] Cooper coaches his teams to have tactical discipline; defensively, he prefers his players to regain possession through composure and aggression.

[54] Cooper cites former Barcelona B coach José Segura as his main influence; the pair worked together at Liverpool's academy.