During the COVID-19 pandemic, most of the deaths in Peru were related to COVID-19; however, cancer deaths have also been exacerbated in the first months of the pandemic. Despite this, excess mortalities of prostate, breast, and uterus cancer are not available by age group and region from January to December 2020. Therefore, we estimated the excess deaths and excess death rates (per 100,000 habitants) due to prostate, breast, and uterus cancer in 25 Peruvian regions. We did a time series analysis. Prostate, breast, and uterus cancer death data for 25 Peruvian regions were retrieved during the COVID-19 pandemic in 2020, as well as data for up to 3 years prior (2017–2019) from the Sistema Informatico Nacional de Defunciones at the Ministry of Health of Peru. Deaths in 2020 were defined as observed deaths. The expected deaths (in 2020) were estimated using the average deaths over 3 preceding years (2017, 2018 and 2019). Excess mortality was calculated as the difference between observed mortality and expected mortality in 2020. We estimated that the number of excess deaths and the excess death rates due to prostate, breast, and uterus cancer were 610 deaths (55%; 12.8 deaths per 100,000 men), 443 deaths (43%; 6 deaths per 100,000 women), and 154 deaths (25%; 2 deaths per 100,000 women), respectively. Excess numbers of deaths and excess death rates due to prostate and breast cancer increased with age. These excess deaths were higher in men aged ≥ 80 years (596 deaths (64%) and 150 deaths per 100,000 men) and women aged 70–79 years (229 deaths (58%) and 15 deaths per 100,000 women), respectively. In summary, during the COVID-19 pandemic, there were excess prostate and breast cancer mortalities in 2020 in Peru, while excess uterus cancer mortalities were low. Age-stratified excess death rates for prostate cancer and breast cancer were higher in men ≥ 80 years and in women ≥ 70 years, respectively.