Pennington has been a member of the religion faculty at Maryville College since 1998. He teaches courses in Hinduism, the culture and history of South Asia, and the study of religion. He conducts research on religion in colonial India, Hindu-Christian encounter, and also writes about method and theory in the study of religion. He is the author of Was Hinduism Invented?: Britons, Indians, and the Colonial Construction of Religion (New York: Oxford University Press, 2005), a study of Hindu-Christian interaction in the the late 18th and early 19th centuries that was reissued in paperback in 2007. He is also the editor of Teaching Religion and Violence (Oxford University Press, 2012), a resource book for college instructors that covers both the history of violence in various religious traditions and contemporary religious conflict. Along with Amy Allocco, he is currently completing a third book, Ritual Innovation in South Asia. Pennington has published articles in the Journal of the American Academy of Religion, the Journal of Hindu-Christian Studies, and Method and Theory in the Study of Religion.

Pennington is a current member of the Advisory Council of the Conference on the Study of Religions and he is a former member of the Board of Directors of the American Academy of Religion, the Board of Directors of the Society for Hindu-Christian Studies of India, and past President of the American Academy of Religion, Southeast Region.