Fowler has received several honorary degrees, including an Honorary Doctorate of Law degree from Simon Fraser University, an Honorary Doctorate of Science degree from Rhodes College, and an Honorary Doctorate of Humanities degree from Oberlin College. He received the Right Livelihood Award with Pat Mooney in 1985 for his work in agriculture and the preservation of biodiversity. Fowler has also received the Vavilov Medal from the Russian Academy of Agricultural Sciences. In 2010, he was one of ten recipients of the 16th Annual Heinz Awards with a special focus on global change. In 2012, he was awarded the "Wind Beneath my Wings" award jointly with his wife Amy P. Goldman at Bette Midler's annual "Hulaween" party. He was the baccalaureate speaker at the 2013 Rhodes College commencement ceremonies and received the 2015 William L. Brown Award for Excellence in Genetic Resource Conservation from the Missouri Botanical Garden.