Allen began his teaching career as an instructor at the University of Minnesota, and later received an appointment as an assistant professor of astronomy at Colgate University in Hamilton, New York, where he taught for twelve years. Allen also worked for the New York State Department of Education from 1940 to 1948, where he eventually became director of the Division of Higher Education. One of his major accomplishments as higher education director, he oversaw the implementation of New York's so-called "emergency colleges"—state supported colleges created to accommodate the influx of returning World War II veterans. Over the course of his teaching and administrative career, Allen authored three textbooks and more than seventy journal articles on such topics as astronomy, higher education and veterans' education.