John Arrillaga is one of five children born into a lower-middle-class home with his mother, Freida, and Father, Gabriel, who traced his roots to the Basque region. He attended Morningside High School in Inglewood, California and graduated in 1955. He attended Stanford University on a basketball scholarship, and was a first-team All-AAWU selection in 1960. He graduated with a bachelor's degree in geography (no longer offered) in 1960, where he was a member of Delta Tau Delta.