Keeping in close touch with a research supervisor is often vital for any university student. Unfortunately, this is hardly possible during the period of a pandemic. In this study, we explored the supervisory challenges that the doctoral students and their research supervisors at a school in a premier university in Uganda experienced and the coping strategies they utilised during the COVID-19 pandemic. We were provoked to undertake the study due to the persistent undocumented complaints from graduate students about their inability to get in touch with their research supervisors because of the closure of the university that was brought about by the pandemic. Taking the interpretive approach, we used a phenomenological research design and collected data by interviewing PhD students and their research supervisors, whom we purposively selected. We analysed the data using the thematic content analysis technique that we based on the factors influencing doctoral research supervision, namely student factors, supervisor factors and institutional factors. Our study findings revealed key research supervisory challenges. At the students’ level, we found loneliness, ICT challenges, unexpected study costs and family disturbances. While at the supervisor’s level, we found inadequate supervisor support and ineffective communication. Yet at the institutional level, we noted unclear institutional research policies and ineffective communication. We therefore concluded that several supervisory challenges negatively affected the students’ doctoral studies during the pandemic. However, there were varied but unclear strategies participants utilised to address these challenges. Hence, we recommend to university leaders to formulate clear institutional graduate training strategies for mitigating disruptions occasioned by any future pandemic.