After retiring as a player Levein became a manager, working at club level for Cowdenbeath, Heart of Midlothian, Leicester City, Raith Rovers and Dundee United.

Levein was appointed Scotland manager in 2009, but he left this position after the team failed to win any of its first four matches in 2014 FIFA World Cup qualification.

After a spell advising Brechin City, Levein was appointed St Johnstone manager in November 2023, before being relieved of his duties in September 2024.

At the age of 15, however, he gave up football for a year, only resuming when his brother, who played for junior club Lochore Welfare invited him to training there.

[8] However, after a poor start to the 2005–06 season, which left the club third from bottom in the Championship relegation zone, he was sacked as manager on 25 January 2006.

[9] Levein was appointed as manager of his boyhood heroes, Scottish Second Division club Raith Rovers, on 5 September 2006, on a non-contract basis.

[10] However, after Dundee United parted company with Craig Brewster, Levein left his non-contract role at Raith Rovers to take up the job at Tannadice.

[11] Levein guided United to four successive home victories, earning him 'Manager of the Month' for November 2006, later repeating the award in March 2007 and again in October 2007.

The club reached the 2008 Scottish League Cup Final, which United led twice before losing to Rangers on a penalty shootout.

Levein overhauled the club's youth system,[14] which subsequently brought through players such as Ryan Gauld and John Souttar.

[16] Scotland won 1–0 in his first match in charge, a friendly against the Czech Republic, with the goal coming from Celtic captain Scott Brown.

[17][19] Levein later said that he had adopted the formation after seeing Russian club Rubin Kazan achieve a good result against FC Barcelona with that approach.

[17] The match ended in a 2–2 draw, after two late controversial penalty kick decisions by Dutch referee Kevin Blom both went against Scotland.

For the 2014 FIFA World Cup, Scotland were drawn into UEFA qualifying Group A with Belgium, Croatia, Macedonia, Serbia and Wales.

[24] Levein stated his belief that Scotland were capable of winning all of their qualifying games, but the first two matches ended in home draws against Serbia and Macedonia.

[17] Levein then recalled Steven Fletcher and Kris Commons, but Scotland fell to two away defeats against Wales and Belgium, which left the Scots bottom of Group A with only 2 points from 4 games.