Mukaiyama has been recognized for his achievements in the form of seven honorary degrees and membership in the national academies of four nations. He is the namesake of the Mukaiyama Award, awarded by the Society of Synthetic Organic Chemistry, Japan since 2005. His major awards include:
* Chemical Society of Japan Award in 1973
* Imperial Prize and Academy Prize from the Japan Academy in 1983
* Nicholaus Copernicus Medal from the Polish Academy of Sciences in 1986
* Person of Cultural Merit from Japan in 1992
* Chevalier de l’Ordre National du Mérite from France in 1994
* ACS Award for Creative work in Synthetic Organic Chemistry from the American Chemical Society in 1996
* Order of Culture from Japan in 1997
* Tetrahedron Prize for Creativity in Organic Chemistry from Elsevier in 1998
* Sir Derek Barton Gold Medal from the Royal Society of Chemistry in 1998