Havemeyer was born in Rye, New York but spent most of his childhood in Hartford, Connecticut after his parents divorced.
In 1907 he went to Sheffield Scientific School at Yale University where he gained a Bachelor of Philosophy in 1910.
He then studied anthropology at Yale and received his MA in 1912 and was awarded a Ph.D. in 1915 for his dissertation "The Drama of Savage Peoples."
He continued to teach as both lecturer and assistant professor, and his subjects included economic geography, social sciences and evolution.
He was awarded the Yale Medal of Honor in 1967 in recognition of his role in the operation of the university.