McKinnon was born in Dundee on 5 August 1970. He started his career with Dundee United, turning professional on 12 August 1986. He soon gained attention as one of the most promising young midfielders in Scottish football. He impressed Brian Clough enough to win a £750,000 move to Nottingham Forest in July 1992, but almost as quickly as he had arrived found himself out of first team contention, Clough deciding that his skilful passing was not what he wanted for his midfield. He left to join Aberdeen on 8 February 1994, costing the Dons £300,000. He returned to Dundee United on 3 November 1995, for a fee of £200,000, where he famously scored a hat-trick of free-kicks in a 3–2 win over Kilmarnock at Rugby Park in February 1997. He remained at Tannadice Park until being released at the end of the 1997–98 season during which he had struggled to gain a first team place. In the close-season he attracted interest from Crystal Palace, as well as French sides Auxerre and Bordeaux, but after initially being on trial, joined Luton Town on 6 August. He left to join Livingston on 12 September 1999, and after an injury hit season and a trial with Wolverhampton Wanderers under Colin Lee, joined Raith Rovers on a short-term contract on 28 July 2000. Raith were unable to meet his wage demands, so he left and began training with Ayr United. He joined Portadown in October 2000, playing one game. In need of first team football to regain his match fitness he joined Stirling Albion on trial on 27 October, playing in the match against Queen's Park at Hampden Park. He joined East Fife, originally as a triallist on 17 November, leaving on 25 January. On 15 March 2001 he joined Torquay United on non-contract terms, but left just five days later without appearing in the first team after the re-emergence of a groin injury. He returned to Torquay as a trialist on 30 July 2001, but along with most of the many players Roy McFarland considered during the round of pre-season friendlies was released without earning a contract. In November 2001 he joined Montrose as a trialist, making his debut in the 1–1 draw with Stirling Albion at Forthbank on 10 November and scoring two weeks later in the 2–1 win over East Fife. Although linked with a return to England to have another attempt at breaking back into full-time football, he signed a deal to stay with Montrose until the end of the season in December 2001. He remained with Montrose until joining Raith Rovers for a second time in January 2003.
Coaching career
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 with 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.
Raith Rovers manager
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 manager
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. Falkirk were later fined by the SPFL for breaching league rules in their recruitment of McKinnon and his assistant Darren Taylor. 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 leaguesfor the first time since 1980. McKinnon was sacked on 16 November 2019, with the team sitting fourth in League One.
Queen's Park
McKinnon became manager of Queen's Park in January 2020. He is the first manager of Queen's Park since the 1980s to secure two wins in his first two matches in charge.
