Tonegawa was born in Nagoya, Japan and attended Hibiya High School in Tokyo. While a student at Kyoto University, Tonegawa became fascinated with operon theory after reading papers by François Jacob and Jacques Monod, whom he credits in part for inspiring his interest in molecular biology. Tonegawa graduated from Kyoto University in 1963 and, due to limited options for molecular biology study in Japan at the time, moved to the University of California, San Diego to do his doctorate study under Dr. Masaki Hayashi. He received his Ph.D. in 1968.