Fahy was named as a Fellow of the Society for Cryobiology in 2014, and in 2010 he received the Distinguished Scientist Award for Reproductive Biology from the Reproductive Biology Professional Group of the American Society of Reproductive Medicine.  He received the Cryopreservation Award from the International Longevity and Cryopreservation Summit held in Madrid, Spain in 2017 in recognition of his career in and dedication to the field of cryobiology. Fahy also received the Grand Prize for Medicine from INPEX in 1995 for his invention of computerized organ cryoprotectant perfusion technology. In 2005, he was recognized as a Fellow of the American Aging Association.