Born in Nara, Japan, Fukui was a lecturer in chemistry at Kyoto Imperial University, becoming professor of physical chemistry from 1951 to 1982. He is noted for his theoretical work on the change in molecular orbitals during reaction, especially reactions of methyl radicals. He also investigated the reaction of molecular nitrogen with transition-metal complexes – a topic potentially important for the fixation of nitrogen.

For his work on frontier orbital theory, Fukui shared the 1981 Nobel Prize for chemistry with Roald Hoffmann.