The current qualitative study attempted to explore the perceptions of doctoral students in relation to the challenges and difficulties they faced during their research degrees. In recent years, substantial and rapid changes have been taking place in the higher educational sector of Pakistan. Most universities have started to place a premium on the enhancement and productivity of research in terms of the number of publications and PhD students’ production. Despite this shift towards a focus on research productivity, universities in general and private universities in particular have been finding it a daunting challenge to provide essential facilities in line with the research needs of students and faculty. The sample of the study comprised of 10 doctoral students, from 5 private sector universities in Peshawar, Khyber Pakhtunkhwa (KP), Pakistan. The sample was selected through purposive and convenient sampling techniques. The data was collected through semi-structured interviews and was analysed using thematic analysis. The current study contributed to the understanding pertaining to the issue in several ways: (1) This study enriched the current literature about writing and reading difficulties of Pakistani doctoral students, (2), The study highlighted loopholes in doctoral studies/courses/programs in Pakistan and identified areas that need revision and improvement to help and improve doctoral studies. The findings revealed several challenges faced by doctoral students. These challenges include academic reading and writing difficulties, lack of requisite computer software application knowledge and skills, problems in supervisors’ role, ill-equipped libraries, and outdated course work content. The study also carries important implications in terms of providing insights into the issues and challenges faced by PhD Education students in Pakistan.