With Queen's Park, MacKinnon won the first three Scottish Cup competitions in 1874, 1875 and 1876 (being no relation of teammate Angus MacKinnon), as well as the first Glasgow Merchants Charity Cup in 1877. He was also capped by Scotland, making nine appearances between 1872 and 1879, scoring five goals. As a player, he was described as "a brilliant dribbling artist".