 Whalen is the founder of the Endangered Language Fund, and served as its president until 2015, when he became Chair of the Board of Directors.He is also a founding member of the Association for Laboratory Phonology and on the advisory board for Healing Through Language, an organization that researches the connection between indigenous language revitalization and physical well-being.From 2006 through 2008, he served as a program officer at the National Science Foundation where he was affiliated with the Cognitive Neuroscience, Documenting Endangered Languages, and Linguistics programs.