The gist of this study was to analyze the supervision challenges that postgraduate students undergo through in course of doing their thesis or project work supervision in universities in Kenya. The purpose of this paper was to explore the challenges that make the process of postgraduate supervision a nightmare to students, consequently, affecting their enthusiasm to learn and successfully complete their studies as scheduled. The objectives of the study were to; ascertain the perceptions of postgraduate supervisee towards supervisory competences of their supervisors, assess the channels of communications between supervisee and supervisors, and establish the availability of supervisors to the supervisee. The paper used a cross section survey design to capture the views of respondents. The study used a sample size (n= 95) which was derived from a target population (N = 198) consisting of; all masters and doctoral students in the School of Education and School of Business & Economics of Kenyatta University and Mount Kenya University respectively. The study used questionnaires to collect data. The main findings of the study were that; supervisors were found to have established friendly interactions with supervisee but did not embrace ICT in supervision, they did not give prompt feedback to their supervisee; and they were hardly accessible to supervisee. The study concludes that; the process of supervision had main challenge of supervisee not receiving timely feedback from their supervisors who had embraced ICT in supervision. This study recommends frequent re-tooling for the supervisors so that they are able to embrace online supervision and hence assist their postgraduate students complete their studies on time. This study is significant as it may inform both the supervisors and supervisee on the best practices of undertaking the process of supervision for both parties to work harmoniously.