Hayashi was born in Kyoto and enrolled at the Imperial University of Tokyo in 1940, earning his BSc in Physics after 2½ years, in 1942.

He was conscripted into the navy[1] and, after the war ended, joined the group of Hideki Yukawa at Kyoto University.

[1] He made additions to the Big Bang nucleosynthesis model that built upon the work of the classic Alpher–Bethe–Gamow paper.

[2] Probably his most famous work was the astrophysical calculations that led to the Hayashi tracks of star formation,[3] and the Hayashi limit that puts a limit on star radius.

He was also involved in the early study of brown dwarfs, some of the smallest stars formed.