There are major structural issues in the higher education system in Pakistan leading to poor governance of institutions and questionable quality of education. An analysis of 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 has been done. 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. The role of the Higher Education Commission of Pakistan as a regulator of higher education in the country and its policies regarding quality assurance have been discussed. This discussion helps in identifying the differences that are present in the governance structures of universities in both sectors. The results have been assessed as to what changes are required to ensure good governance and quality assurance in the universities in Pakistan.