Born in Fukuchiyama, Kyoto in 1928, Shimomura was brought up in Manchukuo (Manchuria, China) and Osaka, Japan while his father served as an officer in the Imperial Japanese Army. Later, his family moved to Isahaya, Nagasaki, 25 km from the epicenter of the August 1945 atomic bombing of the city. He recalled hearing, as a 16-year-old boy, the bomber plane Bockscar before the atom bomb exploded.  The explosion flash blinded Shimomura for about thirty seconds, and he was later drenched by the "black rain" bomb fallout. He overcame great odds in the following 11 years to earn an education and achieve academic success.
Shimomuras education opportunities were starkly limited in devastated, post-war Japan. Although he later recalled having no interest in the subject, he enrolled in the College of Pharmaceutical Sciences of Nagasaki Medical College (now Nagasaki University School of Pharmaceutical Sciences). The Medical College campus had been entirely destroyed by the atomic bomb blast, forcing the pharmacy school to relocate to a temporary campus near Shimomuras home. This proximity was the fortuitous reason he embarked upon the studies and career which would ultimately lead to unanticipated rewards. Shimomura was awarded a BS degree in pharmacy in 1951, and he stayed on as a lab assistant through 1955.
Shimomuras mentor at Nagasaki helped him find employment as an assistant to Professor Yoshimasa Hirata at Nagoya University in 1956. While working for Professor Hirata, he received a MS degree in organic chemistry in 1958 and, before leaving Japan for an appointment at Princeton University, a Ph.D. in organic chemistry in 1960 at Nagoya University. At Nagoya, Hirata assigned Shimomura the challenging task of determining what made the crushed remains of a type of crustacean (Jp. umi-hotaru, lit. "sea-firefly", Vargula hilgendorfii) glow when moistened with water. This assignment led Shimomura to the successful identification of the protein causing the phenomenon, and he published the preliminary findings in the Bulletin of the Chemical Society of Japan' in a paper titled "Crystalline Cypridina luciferin." The article caught the attention of Professor Frank Johnson at Princeton University, and Johnson successfully recruited Shimomura to work with him in 1960.