* 1994 – Progress Award in Synthetic Organic Chemistry, Japan
* 2000 – Division Award of Chemical Society of Japan (Organic Chemistry)
* 2001 – Japan IBM Science Prize
* 2009 – The Commendation for Science and Technology by the MEXT Prizes for Science and Technology
* 2010 – The 7th Leo Esaki Prize
* 2010 – Thomson Reuters Research Front Award
* 2011 – 3M Lectureship Award (The University of British Columbia)
* 2012 – Kharasch Lecturers (The University of Chicago)
* 2013 – Arthur C. Cope Scholar Award
* 2013 – The Chemical Society of Japan (CSJ) Award
* 2013 – Merck-Karl Pfister Visiting Professorship (MIT Lectureship award)
* 2014 – Medal with Purple Ribbon
* 2014 – Fred Basolo Medal (Northwestern University)
* 2018 – Wolf Prize in Chemistry
* 2019 – Paul Karrer Gold Medal
* 2020 – Clarivate Citation Laureate
* 2020 – Chu-Nichi Culture Award
* 2023 – Asahi Prize