After Oxford, Mackinnon became a partner in the family business in Calcutta. He returned to England on the outbreak of World War I and was commissioned into the Royal North Devon Hussars. He transferred to the Scots Guards and serving with them as a lieutenant he was killed in action at Ypres in the Battle of Passchendaele. His remains were not recovered and his name is recorded on the Tyne Cot Memorial nearby.
Mackinnon left a legacy of £80,000 to establish scholarships at Magdalen College which became effective by reversion in 1938.