J. W. de Jong was born in Leiden. He attended primary school and "gymnasium" in Leiden, and went on to study at the University of Leiden from 1939 to 1945, where he began his lifelong study of the "canonical languages" of Buddhism: he took Chinese as his major, while minoring in Japanese and Sanskrit. With the closing of the university in 1940 following the German invasion of the Netherlands, de Jong was forced to continue his studies on his own. With the war's end in 1945, the university reopened and de Jong passed his "candidaatsexamen." In 1946, he traveled to the United States as a visiting professor at Harvard University, where he continued his study of Sanskrit texts.