Huizenga married Dorothy Koeze in 1946. They had two sons and two daughters. One son, Dr. Robert Huizenga, is a prominent physician whose career has included a stint as team physician for the Los Angeles Raiders American football team.
Following his retirement from Rochester, Huizenga and his wife moved to North Carolina, where he continued to serve on advisory committees at major accelerator laboratories, worked to debunk cold fusion, and wrote his memoirs. Dolly Huizenga died in 1999. John Huizenga died of heart failure in San Diego, California, in January 2014, aged 92.