There are major structural issues in the higher education system in Pakistan leading to poor governance of institutions and questionable quality of education. This paper looks at the differences in the role of boards of governors in maintaining quality of education in both the public and the private sector universities in Pakistan. After having conducted qualitative research by interviewing selected academics and by secondary research, the problems in the governance of higher education in the country were identified. Governance in higher education is then analyzed in terms of the Boards of Governors of universities and their role and the overall management and organizational structure of the higher education institutions in both sectors. This paper further explores the role of the Higher Education Commission of Pakistan as a regulator of higher education in the country and its policies regarding quality assurance. This discussion helps in identifying the differences that are present in the governance structures of universities in both sectors. The result has been that the private sector boards portray a more efficient system compared to the public sector boards that lack autonomy and are under strong political influence. The recommendations that have been made require for a change in the organizational structures of boards in the public sector and increased checks by the HEC to promote good governance and quality assurance in universities in the country.