Research plays a significant role in the development of a country. A country cannot progress without establishing a sound research system in its higher education institutions. It is a national dilemma that a conducive research environment could not flourish in Pakistani universities. However, Higher Education Commission (HEC) has been striving hard to promote international level research culture in the country since its establishment. Even though, researchers face so many barriers in conducting research at postgraduate level programs at higher education institutions especially in the provinces which need to be identified and addressed. The purpose of this study was to identify the main barriers and analyze the opinions of supervisors and scholars about various barriers in conducting research at postgraduate level at public and private sector universities of Khyber Pakhtunkhwa. For this purpose eight (08) universities (four each in public and private sector) were randomly selected by the researcher as a sample. The sample consisted of 640 respondents including four each from the disciplines of natural and social sciences. The scholar received 521 responses out of 640. A questionnaire comprising of 50 items and one open ended question was designed. Data was analyzed using mean, percentage, standard deviation and t–test, while open-ended questions were analyzed using content analysis method. The findings of the study revealed that majority of the respondents (supervisors and scholars) were on the same page regarding the barriers (supervisory, financial, social, personal, and administrative) in conducting research at postgraduate level programs in both the sectors. A significant difference of opinions was observed among the views of the respondents about the role of supervisors in public and private universities which may be due to the number of available supervisors and students’ strength. The nature of program did not prove to be a strong variable in producing significant change in the opinions about the barriers except a disagreement was noticed about social barriers among the respondents of public sector universities. There was no difference in the opinion of male and female respondents about barriers in the research process. The discipline of the respondents showed similar responses about the barriers except the data revealed difference of opinions about supervisory barriers in private sector universities. Content analysis revealed that supervisors had reservations about the scholars (passive attitude, lack of academic skills) and administration (lack of HEC approved supervisors, less remuneration, lack of resources) while the scholars too had concerns regarding supervisors (part-time availability, lack of research expertise, paucity of time due to academic and administrative responsibilities) and administration (non-availability of research grant, lengthy topic approval procedure, non-availability of resources, imbalanced supervisor-supervisee ratio). The study concludes by identifying and comparing views of the respondents about the barriers that are creating hurdles in postgraduate research at public and private sector universities of Khyber Pakhtunkhwa as well as suggesting areas where future work might build on the findings of the study.