In 1921, Ishii was commissioned into the Imperial Japanese Army as a military surgeon with the rank of Army Surgeon, First Class (surgeon lieutenant). In 1922, Ishii was assigned to the 1st Army Hospital and Army Medical School in Tokyo, where his work impressed his superiors enough to enable him to return to Kyoto Imperial University to pursue post-graduate medical schooling in 1924. During his studies, Ishii would often grow bacteria "pets" in multiple petri dishes, and his odd practice of raising bacteria as companions rather than as research subjects made him notable to the staff of the university. He did not get along well with his classmates; they would become infuriated as a result of his "pushy behaviour" and "indifference". One of his mentors, Professor Ren Kimura, recalled that Ishii had an odd habit of doing his laboratory work in the middle of the night, using laboratory equipment that had been carefully cleaned by his classmates earlier. His classmates would "really be mad when they came in and found the laboratory equipment dirty the next morning".
