Born in William's Point, in the County of Antigonish, Nova Scotia, the son of John MacKinnon and Eunice MacLeod, MacKinnon's father came to the United States from Eigg, Scotland in 1791 and soon settled in Nova Scotia.

The origins of the university date back to Pope Urban VIII who decided to establish the Urban College with his papal bull Immortalis Dei Filius (August 1, 1627).

From its beginnings, the Urbaniana has always been an academic institution with a missionary character that has served the Catholic Church through the formation of missionaries and experts in the area of Missiology or other disciplines, necessary in the evangelical activity of the Church.

MacKinnon was ordained priest by Archbishop Giacomo Filippo Fransoni on June 4, 1837.

On November 9, 1851, he was appointed Bishop of Arichat by Pope Pius IX.