This research titled, “Evaluation of Education System in Universities of Khyber Pakhtunkhwa and Suggestions to Meet Future Challenges” was a survey research. The objectives of the study were; (i) To evaluate the role of University of Peshawar (UOP) and Gomal University (GU) in imparting higher education in Khyber Pakhtunkhwa (KP), (ii) To compare prevalent physical infrastructure and instructional systems of both the universities, (iii) To examine the evaluation system of both the universities, (iv) To suggest the possible solutions to meet future challenges at university level. The study was delimited to (i) All campuses of University of Peshawar and Gomal University in KP (ii) Academic Sessions 2014-2016 and (iii) Regular faculty xi of both the universities (iv) Faculty of Social Sciences including the Institutes of Education and Research. Other departments are Political Science, Economics, Law, Journalism & Mass-Communication, Arabic & Islamic studies and Institute of Management Studies/ Public Administration which were common in the University of Peshawar and Gomal University D.I.Khan during the survey. From the analysis of data, it was found that at UOP classrooms were well equipped and furnished and provisions of all electronic facilities such as multimedia, internet and PowerPoint were available for effective teaching learning process. Whereas in Gomal University classrooms were not well equipped and furnished. At University of Peshawar departmental library fulfilled the needs of the students regarding provision of relevant/reference books and other facilities. While in Gomal University departmental library did not fulfill the needs of the students. Curriculum of the both universities at various educational levels was at par with other national universities. At UOP priority was given to research by providing adequate research facilities such as grant for research activities and organization of national/international research conferences, whereas GU did not provide such facilities to the faculty. The study recommends that physical facilities such as furnished classrooms, IT rooms, labs, multimedia, internet and stationary shop may be provided through developmental funds to the students and faculty of Gomal University. Further university management may do efforts to enhance the funding from HEC, philanthropists and national/international donors. Further it is recommended that as library is a major source of knowledge and information for students and faculty. Therefore the departmental libraries of Gomal University may be provided with adequate subject books/reference books, ejournals/ books and PCs with internet access for students and faculty by allocating adequate funds. Research is a major function of the university. Therefore the study recommends that priority may be given for provision of research facilities such as grant for research activities and organization of national/international research conferences in Gomal University by allocating adequate funds for research from HEC and other donor agencies.