Purpose: Clinical rotations of medical students across the world have inevitably been affected due to the coronavirus disease 2019 (COVID-19) pandemic. The aims of this study were to explore medical students’ perception on the school’s response and management of clinical rotation during the COVID-19 pandemic and on how it had affected the quality of their education. Methods: An online questionnaire was distributed to third year medical students at one institution whose clinical rotations re-started during the pandemic. The questions asked about the students’ satisfaction with the school’s policy and feelings of safety, and the impact of COVID-19 on clinical learning. Results: The students’ perception on the school’s response to the pandemic was mixed. Re-commencement of the clinical rotations and procurement of personal protective equipment was positive but a third of students still felt unsafe. The decreased number of hospital patients did not seem to have impacted their overall clinical education with praise on the role of the supervising physicians. Seventy-six-point seven percent of students conferred the positive educational opportunities on medical professionalism presented to them only as the clinical rotation during the ongoing pandemic. Conclusion Our observations on the re-commencement of clerkship during this pandemic may help equip medical institutions on future public health crisis.