COVID-19 has had a profound impact on global mortality and morbidity, yet only a fraction of deaths was confirmed and reported. We estimated all-cause excess mortality from 1 January 2020 to 31 December 2022 in the Federation of Bosnia and Herzegovina (FBiH) to assess the true magnitude of the pandemic. Data for this analysis was sourced from the FBiH mortality register and supplemented with population statistics and official COVID-19 death counts (i.e., cases where COVID-19 was registered as the cause of death). Using a Poisson model, all-cause excess number of deaths and rates per 100,000 person-years, adjusted for registration delays and stratified by age and gender, were calculated. FBiH experienced three periods of excess all-cause mortality throughout the first 3 years of the pandemic, with a total of 12,000 excess deaths, highest among adults 45-74 years and males. No excess mortality was observed in children <15 years. The true mortality impact of COVID-19 in FBiH was substantially higher than the reported deaths, including among younger adults. Strengthening civil registration and vital statistics, including establishment of all-cause mortality surveillance, is essential for improved monitoring of future pandemics and other important public health events. A detailed review of the direct and indirect effects of COVID-19 on mortality should be conducted to identify areas that require more resources, improve health provision and inform mitigation efforts in future pandemics to save lives.