Kenyon has received many honors, including the King Faisal Prize for Medicine, the Association of American Medical Colleges Award for Distinguished Research, the Ilse & Helmut Wachter Award for Exceptional Scientific Achievement, and La Fondation IPSEN Prize, for her findings. She is a member of the U.S. National Academy of Sciences and the American Academy of Arts and Sciences. She was President of the Genetics Society of America for 2003. She is also one of featured biologists in the 1995 science documentary Death by Design / The Life and Times of Life and Times.