Mackie was educated at Middlesbrough High School and Jesus College, Oxford where he obtained a first-class degree in History. He was appointed as a Lecturer in History at the University of St Andrews in 1909, aged only twenty-two.
During the First World War, he served in the Argyll and Sutherland Highlanders and was awarded a Military Cross. He was wounded in both the stomach and on the shoulder; these injuries caused him considerable pain for the remainder of his life. He returned to St Andrews after the war, before being appointed Professor of Modern History at Bedford College, University of London, in 1926.
He was Professor of Scottish History and Literature at the University of Glasgow from 1930 to 1957. It was during these years that he wrote The Early Tudors 1485-1558 (Oxford University Press). An influential volume, The Earlier Tudors was a new analysis of Tudor administration - the business of government. In 1957 he retired, and was appointed Historiographer Royal for Scotland.