Born in Kobe, Japan, Yamamoto earned a B.S. at Kyoto University in 1967 and a Ph.D. at Harvard University in 1971. 
He was a professor at Nagoya University from 1983 until 2002 and has since been a professor within the Department of Chemistry at the University of Chicago. His research work is largely in the chemistry of acid catalysts that play an important role in triggering or driving chemical reactions, specifically Lewis and Brønsted acid catalysts used in selective organic synthesis. Yamamoto has authored or co-authored several books on topics in modern synthetic organic chemistry. As of 2021, his h-index equals to 120 with more than 64,000 citations.