Following his graduation from Kyoto Imperial University in 1941, Fukui was engaged in the Army Fuel Laboratory of Japan during World War II.

In 1943, he was appointed a lecturer in fuel chemistry at Kyoto Imperial University and began his career as an experimental organic chemist.

In 1952, Fukui with his young collaborators T. Yonezawa and H. Shingu presented his molecular orbital theory of reactivity in aromatic hydrocarbons, which appeared in the Journal of Chemical Physics.

The frontier orbitals concept came to be recognized following the 1965 publication by Robert B. Woodward and Roald Hoffmann of the Woodward-Hoffmann stereoselection rules, which could predict the reaction rates between two reactants.

Fukui had acknowledged in his Nobel lecture that, 'It is only after the remarkable appearance of the brilliant work by Woodward and Hoffmann that I have become fully aware that not only the density distribution but also the nodal property of the particular orbitals have significance in such a wide variety of chemical reactions.'

In an interview to New Scientist magazine in 1985, Fukui had been highly critical on the practices adopted in Japanese universities and industries to foster science.

In another interview with The Chemical Intelligencer he further elaborates on his criticism by saying, "As is known worldwide, Japan has tried to catch up with the western countries since the beginning of this century by importing science from them."

Fukui was awarded the Nobel Prize for his realization that a good approximation for reactivity could be found by looking at the frontier orbitals (HOMO/LUMO).

From these observations, frontier molecular orbital (FMO) theory simplifies reactivity to interactions between HOMO of one species and the LUMO of the other.