BackgroundSince March 2020, the COVID-19 pandemic has shocked health systems worldwide. This analysis investigated the effects of the pandemic on basic health services utilization in the Democratic Republic of the Congo (DRC) and examined the variability of COVID effects in the capital city Kinshasa, in other urban areas, and in rural areas.MethodsWe estimated time trends models using national health information system data to replicate pre-COVID-19 (i.e., January 2017–February 2020) trajectories of health service utilization, and then used those models to estimate what the levels would have been in the absence of COVID-19 during the pandemic period, starting in March 2020 through March 2021. We classified the difference between the observed and predicted levels as the effect of COVID-19 on health services. We estimated 95% confidence intervals andp-values to examine if the effect of the pandemic, nationally and within specific geographies, was statistically significant.ResultsOur results indicate that COVID-19 negatively impacted health services and subsequent recovery varied by service type and by geographical area. COVID-19 had a lasting impact on overall service utilization as well as on malaria and pneumonia-related visits among young children in the DRC. We also found that the effects of COVID-19 were even more immediate and stronger in the capital city of Kinshasa compared with the national effect. Both nationally and in Kinshasa, most affected services had slow and incomplete recovery to expected levels. Therefore, our analysis indicates that COVID-19 continued to affect health services in the DRC throughout the first year of the pandemic.ConclusionsThe methodology used in this article allows for examining the variability in magnitude, timing, and duration of the COVID effects within geographical areas of the DRC and nationally. This analytical procedure based on national health information system data could be applied to surveil health service disruptions and better inform rapid responses from health service managers and policymakers.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12913-023-09547-9.