This dataset originates from a study that examined the effects of public health emergencies on research regulatory systems in Uganda, using the COVID-19 pandemic as a case study. The study explored stakeholders’ experiences and perceptions regarding the implementation of clinical research policies and guidelines, and how these influenced the conduct of ethical, safe, and timely research during the pandemic. In particular, the study assessed perceived facilitators, barriers, and regulatory adaptations introduced to sustain research oversight and operations under emergency conditions. Documenting these experiences and perspectives, the study provides important evidence to inform the strengthening of resilient, adaptive, and responsive research governance frameworks for future public health emergencies in Uganda and similar settings.