In 1951, Cowen returned to Australia to become dean of the law faculty at the University of Melbourne. In 1953, still while at The University of Melbourne, he was awarded a Fulbright Senior Scholarship in Law to Harvard University. He became known as an expert on constitutional law, and was a visiting professor at a number of overseas institutions. He later served as vice-chancellor of the University of New England (1966–1970) and the University of Queensland (1970–1977). In 1977, Malcolm Fraser appointed Cowen to succeed John Kerr as governor-general. He was an uncontroversial choice, and became the second Jewish holder of the position, after Sir Isaac Isaacs. After leaving office, Cowen returned to academia, serving as provost of Oriel College, Oxford, from 1982 to 1990.