Introduction: Amidst the chaos of COVID-19, health care practitioners are persistently providing services and experiencing many challenges. This study aimed to determine the perception of health care practitioners of government designated COVID-19 hospitals of Nepal towards the management of COVID-19 pandemic. Methods: A descriptive cross-sectional study was conducted among the frontline health care practitioners working in the government designated COVID-19 hospitals in Nepal from 21st June, 2020 to 15th August, 2020. Ethical approval was obtained from the Ethical Review Board of the Nepal Health Research Council (Reference number: 347/2020 P). A total of 252 health care practitioners (doctors, nurses, and paramedics) working at the forefront in the emergency ward, general wards, intensive care units, isolation centers, fever clinics, laboratory, quarantine centers, help desks, etc. in the designated hospitals who consented to participate were included in the study. Convenience sampling was used. The data was analyzed using Statistical Package for the Social Sciences version 16.0. Point estimate at 95% confidence interval was calculated along with frequency and proportion for binary data. Results: Only 41 (16.3%) (11.73-20.86 at 95% Confidence Interval) of the health care practitioners were found to have satisfactory perception towards the management of COVID-19 pandemic in Nepal. Conclusions: The satisfactory perception of the health care practitioners in our study towards the management of COVID-19 pandemic in Nepal is lower as compared to the other studies in Nepal and abroad.