COVID-19 has had a devastating impact on preventable and treatable pediatric diseases in Ethiopia. This study looks at the impact of COVID-19 on pneumonia and acute diarrheal diseases in the country, as well as the differences between administrative regions. In Ethiopia, we conducted a retrospective pre-post study to assess the impact of COVID-19 on children under the age of five who had acute diarrhea and pneumonia and were treated in health facilities during the pre-COVID-19 era (March 2019 to February 2020) and the COVID-19 era (March 2020 to February 2021). From the National Health Management District Health Information System (DHIS2, HMIS), we retrieved data on total acute diarrheal disease and pneumonia, along with their regional and monthly distribution. We calculated incidence rate ratios comparing the rates of acute diarrhea and pneumonia during the pre-and post-COVID-19 eras and adjusted for the year, using Poisson regression. The number of under-five children treated for acute pneumonia decreased from 2,448,882 before COVID-19 to 2,089,542 ((14.7% reduction (95%CI;8.72–21.28), p<0.001)) during COVID-19. Similarly, the number of under-five children treated for acute diarrheal disease decreased from 3,287,850 in pre-COVID-19 to, 2,961,771((9.91% reduction (95%CI;6.3–17.6%),p<0.001)) during COVID-19. In the majority of the administrative regions studied, pneumonia and acute diarrhea diseases decreased during COVID-19, but they increased in Gambella, Somalia, and Afar. During the COVID-19 period, the greatest reduction of children with pneumonia (54%) and diarrhea disease (37.3%) was found in Addis Ababa (p<0.001). The majority of administrative regions included in this study have seen a decrease in pneumonia and acute diarrheal diseases among children under the age of five, while three regions namely, Somalia, Gambela, and Afar saw an increase in cases during the pandemic. This emphasizes the importance of using tailored approaches in mitigating the impact of infectious diseases such as diarrhea and pneumonia during situations of a pandemic such as COVID-19.