Huehnergard was born in Kitchener, Ontario, Canada, and was raised in the nearby city of Waterloo, Ontario. He graduated from the Kitchener–Waterloo Collegiate and Vocational School in 1970. He received a B.A. from Wilfrid Laurier University in 1974 and a Ph.D from Harvard University in 1979, where he studied with William L. Moran, Thomas O. Lambdin, and Frank Moore Cross.