INTRODUCTION: COVID-19 had caused nearly 12,000 deaths in Nepal by March 2023. In this study, we compare COVID-19-associated mortality in the first (September 15 to November 30, 2020) and second (April 15 to June 30, 2021) waves of the pandemic in Nepal and investigate the associated epidemiological factors. METHODS: We disaggregated the COVID-19-related deaths between the first and second waves of the pandemic using the national COVID-19 database and evaluated the association of independent variables with the deaths in the first versus second waves. RESULTS: Out of 8133 deaths, 25% died in the first wave and 75% in the second. Overall, 33.5% of the deceased were female, and 52% of the deaths were in those 60 years or older. A vast majority (92%) of deaths occurred in hospitals. Geographically, the middle "Hill" region (58.3%) witnessed the most significant number of deaths. About two thirds (64%) had at least one comorbid condition. Multivariable logistic regression showed a difference in the reported deaths by province (state) and geography (ecological region) between the first and second waves. Those in the age groups "19-39 years" and "40-59 years" were more likely to die in the second wave than in the first wave compared to the younger age group. CONCLUSIONS: Overall, deaths were concentrated among older age groups, males, in the Hill regions, in the western provinces, and those with comorbidities. Therefore, the country must focus on these areas to ensure an efficient and effective pandemic response in the future.