Houk received the Akron American Chemical Society (ACS) Section Award in 1984. He was awarded the Arthur C. Cope Scholar Award of the ACS in 1988, the James Flack Norris Award in Physical Organic Chemistry of the ACS in 1991, the Schrödinger Medal of the World Association of Theoretically Oriented Chemists (WATOC) in 1998, the Tolman Medal of the Southern California Section of the ACS in 1998, the ACS Award for Computers in Chemical and Pharmaceutical Sciences in 2003, the Arthur C. Cope Award of the ACS in 2010, the Robert Robinson Award of the Royal Society of Chemistry in 2012, and UCLA’s Glenn T. Seaborg Award in 2013.