ObjectiveIn this study, we assess the indirect impact of COVID-19 on utilisation of immunisation and outpatient services in Kenya.DesignLongitudinal study.SettingData were analysed from all healthcare facilities reporting to Kenya’s health information system from January 2018 to March 2021. Multiple imputation was used to address missing data, interrupted time series analysis was used to quantify the changes in utilisation of services and sensitivity analysis was carried out to assess robustness of estimates.Exposure of interestCOVID-19 outbreak and associated interventions.Outcome measuresMonthly attendance to health facilities. We assessed changes in immunisation and various outpatient services nationally.ResultsBefore the first case of COVID-19 and pursuant intervention measures in March 2020, uptake of health services was consistent with historical levels. There was significant drops in attendance (level changes) in April 2020 for overall outpatient visits for under-fives (rate ratio, RR 0.50, 95% CI 0.44 to 0.57), under-fives with pneumonia (RR 0.43, 95% CI 0.38 to 0.47), overall over-five visits (RR 0.65, 95% CI 0.57 to 0.75), over-fives with pneumonia (RR 0.62, 95% CI 0.55 to 0.70), fourth antenatal care visit (RR 0.86, 95% CI 0.80 to 0.93), total hypertension (RR 0.89, 95% CI 0.82 to 0.96), diabetes cases (RR 0.95 95% CI, 0.93 to 0.97) and HIV testing (RR 0.97, 95% CI 0.94 to 0.99). Immunisation services, first antenatal care visits, new cases of hypertension and diabetes were not affected. The post-COVID-19 trend was increasing, with more recent data suggesting reversal of effects and health services reverting to expected levels as of March 2021.ConclusionCOVID-19 pandemic has had varied indirect effects on utilisation of health services in Kenya. There is need for proactive and targeted interventions to reverse these effects as part of the pandemic’s response to avert non-COVID-19 indirect mortality.