Junior football and Brechin City McKinnon moved to
Lochee United in 2004, before leaving in July 2005 to take up a player/coach position with
Broughty Athletic. McKinnon returned as Lochee manager in 2006. He was linked with the managerial posts at both
Brechin City and
Montrose in December 2008, with Lochee stating their desire that he stay until at least the end of their run in the Scottish FA Cup. On 16 July, McKinnon was appointed the new Technical Development Officer of the
Scottish Football Association. He replaced Mark McNally, who became assistant manager at
Scottish First Division club
Morton. McKinnon was appointed manager of
Scottish Second Division club
Brechin City on 9 October 2012. They finished in third, eighth and fourth place in the third tier in his three seasons at the club.
Raith Rovers On 23 May 2015, it was confirmed that McKinnon had been appointed manager of
Raith Rovers. McKinnon guided Raith to fourth place in the
2015–16 Scottish Championship, qualifying for the promotion playoffs. He resigned on 11 May, after entering discussions with
Dundee United about their managerial vacancy.
Dundee United On 12 May 2016,
Dundee United announced that they had appointed McKinnon as their manager on a three-year contract. In his first season in charge, United won the
2017 Scottish Challenge Cup Final, beating
St Mirren 2–1. They went on to finish third in the Championship and qualified for the promotion playoffs. They progressed to the final by beating
Morton and
Falkirk, but lost 1–0 to
Hamilton in the final. United sacked McKinnon in October 2017, after losses to
Livingston and
Inverness left them in fourth place.
Morton McKinnon was appointed manager of
Scottish Championship club
Greenock Morton on 30 May 2018, and he appointed long-term deputy Darren Taylor as his 'first team coach'. The first match of his reign as Morton manager was a 0–0 draw in a friendly away to
Forfar Athletic. On 31 August 2018, after holding a Morton training session in the morning, McKinnon agreed to take over at their Championship rivals
Falkirk. In the following October, on Falkirk's first visit to Cappielow with McKinnon in charge, Morton fans greeted McKinnon with "
Judas" branded red card posters provided by the
Greenock Telegraph newspaper.
Falkirk McKinnon was appointed
Falkirk manager on 31 August 2018. Under his management, Falkirk were relegated to the third tier of the
Scottish leagues for the first time since 1980.
Queen's Park McKinnon became manager of
Queen's Park in January 2020. He became the first manager of Queen's Park since the 1980s to secure two wins in his first two matches in charge, and the team won
2020–21 Scottish League Two (and promotion to League One) under his management. McKinnon left the club after the 2020–21 season had ended. In July 2023, he was given permission to speak to
EFL League Two club
Forest Green Rovers, with a view to becoming assistant manager to his former Dundee United team mate,
Duncan Ferguson. The move fell through when Ferguson was sacked as Forest Green manager, and McKinnon resumed his role at Forfar. He left the club in November 2024 following a 3-0 home defeat by
The Spartans with the club sitting bottom of
League Two.
Brechin City (second spell) McKinnon returned to Brechin City, now in the
Highland League, in March 2025, when he was appointed as interim manager for the last nine games of the
2024–25 season. ==Career statistics==