Background Coronavirus disease 2019 (COVID-19) altered healthcare utilization patterns. However, there is a dearth of literature comparing methods for quantifying the extent to which the pandemic disrupted healthcare service provision in sub-Saharan African countries. Objective To compare interrupted time series analysis using Prophet and Poisson regression models in evaluating the impact of COVID-19 on essential health services. Methods We used reported data from Uganda’s Health Management Information System from February 2018 to December 2020. We compared Prophet and Poisson models in evaluating the impact of COVID-19 on new clinic visits, diabetes clinic visits, and in-hospital deliveries between March 2020 to December 2020 and across the Central, Eastern, Northern, and Western regions of Uganda. Results The models generated similar estimates of the impact of COVID-19 in 10 of the 12 outcome-region pairs evaluated. Both models estimated declines in new clinic visits in the Central, Northern, and Western regions, and an increase in the Eastern Region. Both models estimated declines in diabetes clinic visits in the Central and Western regions, with no significant changes in the Eastern and Northern regions. For in-hospital deliveries, the models estimated a decline in the Western Region, no changes in the Central Region, and had different estimates in the Eastern and Northern regions. Conclusions The Prophet and Poisson models are useful in quantifying the impact of interruptions on essential health services during pandemics but may result in different measures of effect. Rigor and multimethod triangulation are necessary to study the true effect of pandemics on essential health services.