The major structural issues in higher education system of Pakistan are leading to poor governance of the educational institutions and questionable quality of education. Governance differences are present both in public and private sector universities. The private sector board portrays a more efficient system compared to the public sector board that lacks autonomy and is under strong political influence. In most of the private and public sector universities in Pakistan, the board of governors is a combination of alumni, donors, appointees, public figures, government nominees etc. It is very rare to find a member on the board being appointed because they possess knowledge of how universities need to perform or they have outstanding academic contribution. According to World Bank Report (2000) Pakistan has a high level of accountability but it is of negative kind. This negativity is a reflection of the high government control on the appointment of board members of public sector universities. The board of governors has a low degree of autonomy. Private sector universities in Pakistan have grown by a large number in the last two decades. However, at one end, the growth of such institutions provides more variety to students; there are some universities with questionable status. Quality Assurance for the academia as well as the government and policymakers is essential to guarantee outcomes for the managing of higher education institutions (HEIs). Quality can be assured by extrinsic and intrinsic factors – inspection and accountability are externally monitored, whereas teachers, a variety of programs etc derive quality internally in institutions. HEC has acted like any other bureaucracy in the country where polices are made on the basis of a reaction to the problem rather than to actually finding the cause of the problem. Higher education institutions are still in confusion. Unfortunately, a coherent policy for higher education in the country has not been formulated at the national level. This has then led to the inability to handle the issue of governance in the country as no decision has been taken for monitoring higher education institutions, although federal or provincial governments should have authority over universities. HEC has acted like any other bureaucracy in the country where polices are made on the basis of a reaction to the problem rather than to actually finding the cause of the problem. Organisational structure issues are the main cause of inefficiency of higher education institutions. Institutional autonomy should be advanced in a context which seeks greater accountability from institutions and a more systematic approach to the structure of higher education institutions. The board of governors of universities seems unaware of these structural issues of universities. This leads to universities being unable to cope with the challenges. These challenges include the evolution of new markets and the creation of new professions and vocations. Governance issues at structural, academic, and organisational level are hindrances in quality education. Universities remain so overly centralised that decision making remains distorted. There is a need for decentralisation in terms of decision making. Unfortunately in majority of the universities in Pakistan, emphasis is only placed on teaching leading to large class sizes and high teaching loads leaving no room for proper research. On academic level there must be right balance between research and teaching, since research is essential for the development of faculty and the improvement of teaching. Unfortunately in majority of the universities in Pakistan, emphasis is only placed on teaching leading to large class sizes and high teaching loads leaving no room for proper research. Higher education system in Pakistan is far from developed. The issue of governance and the role of board of governors in both the public and the private sectors are critical and there is need for better management to ensure quality assurance. Higher Education in Pakistan is not at par with international standards leaving a dearth of qualified graduates who can help with the rebuilding of the higher education institutions. There is a need for the public sector’s boards to be remodeled to cope with the changes and to be able to provide good governance. For restructuring of governance of any university in Pakistan, there is a need for both incremental and strategic change. Incremental change happens slowly. There is a need to improve the quality of faculty and the programs being offered. Universities in Pakistan need strategic and organizational change as well which is lot harder than incremental change. There should only be quality programs in universities and programs that are not productive should be halted immediately so that more appropriate and quality basedprograms can be introduced. The bottom line is that there are major issues in governance of universities in Pakistan both in Public and private sectors. The private sector universities are still performing much better than public sector counterparts. The reasonsfor underperformance of public sector universitiesare linked to the level of autonomy that the private sectors enjoy. The administration system also determines the efficiency and quality of education system; it must be supportive. For example, the services provided by Registrar, Examination department, Library, Computer Lab, Faculty office, Rector office, Sports etc. For quality education public sector universities need to restructure the level of board of governors as well as governance through strategic and transitional change. The outcomes may be subtle or slow but it will definitely improve the standards of quality of education in Pakistan over a certain period of time.