Background The Covid-19 pandemic has posed a challenge to organizing a safe clinical assessment for postgraduate degree candidates completing the residency programmes in various specialties. Although minimizing the risk of Covid-19 transmission is a priority, fulfilling the objectives of the assessment is equally important. Methods We conducted this study in the Department of Internal Medicine at our institute. Instead of physically examining patients, case scenarios that included history, clinical and investigational data of the cardiovascular system (CVS) were presented to the candidates. Performance was scored by both the conventional and the CVS objective-structured clinical examination (CVS-OSCE) method and compared. Results Clinical assessment examination of 27 candidates for the degree of Doctor of Medicine showed that the median cumulative score gained in narrating and analysing various differential diagnoses was lower compared to the mean cumulative score gained in arriving at a single correct diagnosis (50% [interquartile range-IQR 39%-64%] v. 79% [IQR 64%-100%], p<0.01). Most of the candidates agreed that case scenarios were good alternatives to the conventional physical examination amidst the pandemic. Conclusion CVS-OSCE-based assessment using structured case scenarios is a feasible and effective alternative for clinical skill assessment in high-stake examinations.