Background There is a worrying lack of epidemiological data on the sex differential in COVID-19 infection and death rates between the regions of Peru. Methods Using cases and death data from the national population-based surveillance system of Peru, we estimated incidence, mortality and fatality, stratified by sex, age and geographic distribution (per 100,000 habitants) from March 16 to November 27, 2020. At the same time, we calculated the risk of COVID-19 death. Results During the study period, 961894 cases and 35913 deaths were reported in Peru. Men had a twofold higher risk of COVID-19 death within the overall population of Peru (odds ratio (OR), 2.11; confidence interval (CI) 95%; 2.06-2.16; p<0.00001), as well as 20 regions of Peru, compared to women (p<0.05). There were variations in incidence, mortality and fatality rates stratified by sex, age, and region. The incidence rate was higher among men than among women (3079 vs. 2819 per 100,000 habitants, respectively). The mortality rate was two times higher in males than in females (153 vs. 68 per 100,000 habitants, respectively). The mortality rates increased with age, and were high in men 60 years of age or older. The fatality rate was two times higher in men than in women (4.96% vs. 2.41%, respectively), and was high in men 50 years of age or older. Conclusions These findings show the higher incidence, mortality and fatality rates among men than among women from Peru. These rates vary widely by region, and men are at greater risk of COVID-19 death. In addition, the mortality and fatality rates increased with age, and were most predominant in men 50 years of age or older.