Résumé : Abstract Background Malaria affects millions of Cameroonian children under 5 years of age living in the North and Far North regions. These regions bear the greatest burden, particularly for children under 5 years of age. To reduce the burden of disease in these regions, Cameroon adopted the Seasonal Malaria Chemoprevention (SMC) in 2016 and has implemented it each year since its adoption. However, no previous studies have systematically assessed the effects of this intervention in Cameroon. It is important to understand its effect and whether its implementation could be improved. This study aimed to assess the effect of SMC in Cameroon during the period 2016–2021 on malaria morbidity in children under 5 years of age using routine data. Methods Data on malaria cases were extracted from the Cameroon Health Monitoring Information System (HMIS) from January 1, 2011, to December 31, 2021. Health facilities report these data monthly on a single platform, the District Health Information System version 2 (DHIS2). Thus, a controlled interrupted time-series model in a Bayesian framework was used to evaluate the effects of the SMC on malaria morbidity. Results SMC implementation was associated with a reduction in the incidence of uncomplicated malaria cases during the high-transmission periods from 2016 to 2021. Regarding the incidence of severe malaria during the high-transmission period, a reduction was found over the period 2016–2019. The highest reduction was registered during the second year of implementation in 2017:15% (95% Credible Interval, 10–19) of uncomplicated malaria cases and 51% (47–54) of confirmed severe malaria cases. Conclusion The addition of SMC to the malaria intervention package in Cameroon decreased the incidence of uncomplicated and severe malaria among children under 5 years of age. Based on these findings, this study supports the wide implementation of SMC to reduce the malaria burden in Cameroon as well as the use of routine malaria data to monitor the efficiency of the strategy in a timely manner.