He rowed for his college and the Magdalen College Coxless four won the Stewards' Challenge Cup and the Visitors' Challenge Cup at Henley Royal Regatta in 1907 and 1908. The Magdalen crew was chosen to represent Great Britain rowing at the 1908 Summer Olympics, and Mackinnon was in the four with Collier Cudmore, John Somers-Smith and James Angus Gillan.
He represented his university through rowing events and the Magdalen College Coxless four won prestigious titles at Henley Royal Regatta in 1907 and 1908. The Magdalen crew was selected to represent Britain in Olympic rowing in 1908, with Mackinnon competing alongside Collier Cudmore, John Somers-Smith, and James Angus Gillan.