Cunningham, known as Jack, received his B.Eng. in Engineering Physics (1950) and M.Sc. in Radiation Physics (1951) from the University of Saskatchewan in Saskatoon. In 1955, he completed his Ph.D. at the University of Toronto in physics. After working for Canada's Defense Research Board, he became a staff Medical Physicist at Toronto's Ontario Cancer Institute / Princess Margaret Cancer Centre in 1958.