He coached three different professional teams in his career; the American Basketball Association's Spirits of St. Louis, and the NBA's Buffalo Braves and New Jersey Nets.
He was an All-High choice in basketball in 1944, 1945, and 1946, and established a Yale Cup scoring record while pacing the Macks to the City Championship as a junior and senior.
In perhaps his greatest moment of individual distinction, MacKinnon edged out College of the Holy Cross's Bob Cousy as MVP of the Jesuit Game in 1949.
He also coached during 1974–75 in the American Basketball Association, leading the Spirits of St. Louis to a stunning upset of the defending champion New York Nets in the semifinals of the 1975 ABA Playoffs.
His son, Bob MacKinnon Jr., has coached in the NBA Development League with the Colorado 14ers, Idaho Stampede, and Los Angeles D-Fenders.