Mukaiyama had a scientific career spanning over sixty years, during which he published over 900 papers. After its founding in 1972, Mukaiyama only published in the Japanese journal Chemistry Letters, citing a belief that "the results of ones chemistry should be published in journals of ones country." The combination of the high quality of his work and the over 600 papers that he published in Chemistry Letters played an important role in its spread to other nations.
A total of 145 people earned their doctorates under Mukaiyama, with 54 eventually becoming professors in various institutions.