John Robert Huizenga was born on a farm near Fulton, Illinois, the son of Henry and Josie (Brands) Huizenga.  He attended Erie High School and Morrison High School, graduating from the latter in 1940.  He continued his education at Calvin College in Michigan, from which he received a bachelors degree in 1944.  He would maintain his ties to Calvin later in life, for example collaborating on fundamental nuclear research with his Calvin friend Roger Griffioen, who had gone on to become a professor there.  Calvin would name him one of the colleges Distinguished Alumni in 1975.
Along with other Calvin students, he was recruited after graduation to work for the Manhattan Project, at the Project's site in Oak Ridge, Tennessee, that was dedicated to the production of highly enriched uranium.  Following his time in Oak Ridge, he continued his education at the University of Illinois, receiving a Doctor of Philosophy degree in physical chemistry in 1949. On completing his studies he held joint appointments at the University of Chicago and Argonne National Laboratory.