After a spell coaching at Aston Villa, Clarke was appointed Kilmarnock manager in October 2017 and led them to a European place with a club record points total in his only full season in charge.

Speaking in February 2019, Clarke said he was thankful that Chelsea had signed him as it meant that he and his family no longer had to live with religious sectarianism in the west of Scotland.

[citation needed] Clarke was caretaker manager following Gullit's resignation,[15] taking charge of one match, a 5–1 defeat against Manchester United.

[19] When Mourinho left Chelsea in September 2007, Clarke's services were retained by Avram Grant, although Henk ten Cate was brought in as another assistant coach.

[20][21] BBC Sport and The Times both reported then that although Clarke remained on the Chelsea coaching staff, he would be looking to pursue opportunities to become a manager in his own right.

[20][21] Chelsea assured Clarke of his status, citing his loyalty, popularity amongst the club's supporters and work in the aftermath of Mourinho's departure.

[31] Albion began the Clarke era with a 3–0 home win against Liverpool on the opening day of the 2012–13 Premier League season.

Clarke suffered his first competitive defeat away at Fulham, but West Brom soon jumped back with 1–0 home victory over Reading.

In November, the club won four consecutive matches in a row for the first time since 1980, defeating Southampton, Wigan Athletic, Chelsea and Sunderland.

During the January transfer window, Clarke encountered some problems with want-away Nigerian Striker Peter Odemwingie, who desired a move to Queens Park Rangers, but West Brom refused to sell.

[37] West Brom ended the season in style with a dramatic 5–5 draw with Manchester United, in what was Sir Alex Ferguson's final match as manager.

Clarke and West Brom returned for the new season with a 1–0 home loss to Southampton at The Hawthorns following a 90th-minute Rickie Lambert penalty.

[46] Clarke was hired by Aston Villa on 2 June 2016 to be their assistant manager, working alongside former Chelsea teammate Roberto Di Matteo.

[51] Following the league's winter break, Kilmarnock recorded a home victory over leaders Celtic, with Youssouf Mulumbu scoring the only goal to inflict what was only the second domestic defeat on the Glasgow club's manager Brendan Rodgers.

[54] Clarke continued his impressive work the next season, including another win over Celtic and two over Rangers,[55] culminating in a third-place finish and European qualification for Kilmarnock.

[58] Immediately after the league season ended, Clarke left Kilmarnock to take the national team manager position.

[7] In May 2019, Clarke was appointed manager of the Scotland national team on a contract due to run until the end of 2022 FIFA World Cup qualification.

[59] The team then suffered four consecutive defeats against Belgium and Russia, two of them by 4–0 margins, which ended any hope of qualifying automatically for Euro 2020.

[60] On 12 November 2020, Scotland defeated Serbia 4–5 on penalties after a 1–1 draw to take their place in the delayed finals via the UEFA Nations League route, their first major tournament since 1998.