The study was descriptive in nature dealt with comparative analysis of MPhil/PhD Education Programmes in Public & Private Sector Universities of Khyber Pakhtunkhwa (KP), Pakistan. The population of the study was all twenty five (25) recognized universities of KP province at present. The sample was purposively selected from both sectors universities and the reason was that all universities did not have MPhil/PhD programmes in Education. Total Six (06) Universities (03 from public and 03 from private sectors) were the sample of the study. The research objectives were: (1) to make a comparative analysis of MPhil/ PhD Education programmes of selected universities in KP in terms of input process and output. (2) To explore the weaknesses and strengths of MPhil/ PhD Education programmes & (3) to make viable recommendations for improvement and strengthening of the MPhil/PhD programmes of these universities. The study intended to find out the answers to these research questions: (1) what are the current practices in both public and private sector universities in MPhil/PhD Education programmes? (2) What are the strengths and weaknesses in MPhil/PhD Education programmes in sampled universities? & (3) what recommendations the study can make for the improvement of these programmes? Tools used for data collection were questionnaires and interviews. Questionnaires were used for academicians and research scholars, while interviews were conducted from the Chairman Department of Education, Controller of Examinations and Registrars of the sampled universities. The major findings were: that all the sampled universities have all the basic requirements, human resources and other required facilities for MPhil/PhD Programmes as per Higher Education Commission guidelines. The administration of all sampled universities did not take required interest in conducting seminars, workshops and conferences to develop research culture and skills of the research scholars. The problems of internal politics and grouping in both sectors universities were visible which resulted in delaying of approval of synopses from the boards of research committee. Teachers did not work properly on different aspects of research and report writing in the class for improving the quality of research. The study concluded that Public sector universities were performing slightly better than private sector universities in terms of appointment; staff promotion; staff facilities; provision of financial assistance; relations with HEC, provision of scholarships to scholars and faculty, and College affiliation. A significant difference among these universities in terms of research was noted. The research supervision process was quick and fast in private sector universities as compared to public sector universities. The study recommended that: Private universities research scholars should be provided HEC scholarships for encouragements. The curriculum at MPhil and PhD levels should be upgraded and may be made compatible to the developed countries. Research related workshops and seminars should be conducted on regular basis. Promotion of faculty members may be made on the basis of research publication and research supervisions. The teaching learning environment at universities level may be made students friendly. The universities administrative and teaching staff may be made free from malpractices, nepotisms and favoritisms. Staff hiring may be made transparent.