An alumnus of St Saviour's Roman Catholic High School, as a player McKinnon was a midfielder for such clubs as Dundee United, Nottingham Forest, Aberdeen, Livingston, Raith Rovers and Montrose.
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.
In the close-season he attracted interest from Crystal Palace, as well as French sides Auxerre and Bordeaux, but joined Luton Town on 6 August.
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.
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 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.
[17] On 31 August 2018, after holding a Morton training session in the morning, McKinnon agreed to take over at their Championship rivals Falkirk.
[18] Falkirk were later fined by the SPFL for breaching league rules in their recruitment of McKinnon and his assistant Darren Taylor.
[24] On 10 November 2022, McKinnon was named as the new manager of Scottish League Two club Forfar Athletic on a rolling contract until 2025.