Background: Malaria remains a leading cause of morbidity and mortality among children under five years of age in sub-Saharan Africa. Nigeria bears the highest global malaria burden, accounting for 25.9% of global cases and 30.9% of global malaria deaths in 2023 (World Health Organization [WHO], 2024). Northern Nigeria carries a disproportionate share of this burden, with transmission peaking between July and October. Seasonal malaria chemoprevention (SMC) with sulfadoxine-pyrimethamine plus amodiaquine (SP+AQ) is a WHO-recommended strategy for eligible children in the Sahel sub-region, yet rigorous programmatic impact assessments anchored in Nigerian routine health data remain limited.

Objective: To assess the impact of SMC on confirmed malaria incidence, test positivity rate (TPR), malaria-related admissions, and inpatient malaria deaths among under-five children across three states in Northern Nigeria  –  Kano State (North-West), Yobe State (North-East), and Niger State (North-Central)  –  from January 2020 to December 2024.

Methodology: A retrospective cross-sectional design was applied to secondary data from 360 purposively selected primary healthcare facilities across three states: Kano State (North-West zone; n=120), Yobe State (North-East zone; n=120), and Niger State (North-Central zone; n=120). Pre-SMC (January-June) and intra-SMC (July-October) periods were compared over five consecutive years using negative binomial regression, chi-square tests, and Joinpoint trend analysis. Ethical approval was obtained from the respective State Ministries of Health Research Ethics Committees in Kano, Yobe, and Niger States.

Results: Mean SMC coverage across the study period ranged from 75.1% (Yobe) to 77.4% (Kano) and 74.8% (Niger State). Pooled across all three states and five years, confirmed malaria incidence was 46.3% lower during intra-SMC versus pre-SMC periods (incidence rate ratio [IRR] = 0.537; 95% CI: 0.501-0.575; p < 0.001). The pooled test positivity rate fell from 60.7% (pre-SMC) to 34.9% (intra-SMC). Malaria-related admissions declined by a pooled 40.9% during SMC periods. Impact strengthened progressively from 2020 to 2023 across all three states alongside improving coverage, with a slight attenuation in 2024. Inter-state variation was evident: Kano achieved the largest pooled reduction (48.5%), followed by Niger State (45.8%) and Yobe (44.6%).

Conclusion: SMC delivers substantial and measurable reductions in the malaria burden among under-five children under operational conditions across geographically and ecologically diverse states in Northern Nigeria. The consistency of findings across the North-West, North-East, and North-Central zones strengthens the evidence base for programme-wide policy. Sustained coverage above 80%, targeted support for later delivery cycles, and reinforced supply chain management are essential to consolidating programme gains. These multi-state findings support continued prioritisation of SMC within Nigeria’s National Malaria Strategic Plan 2021-2025.