Background: Few longitudinal studies have examined the long-term health impact of changing malaria prevention and treatment strategies in Africa. This study analyses 35 years of clinical surveillance among paediatric malaria admissions in Kilifi, Kenya. Methods: Children aged 1 month to 14 years who were residents of rural Kilifi Health and Demographic Surveillance System and admitted to Kilifi County Hospital between January 1990 and December 2024 were included. Community malaria exposure was estimated using infection prevalence among children admitted for trauma, elective surgery, bites and neoplasms. Malaria admissions were defined as hospitalisations with a positive blood slide and a primary, secondary, or co-morbid malaria diagnosis. Severe malaria phenotypes including severe anaemia, cerebral malaria, hyper-parasitaemia and in-hospital mortality were also examined. Binomial and Poisson regression models assessed temporal differences, using 1990 to 1996 as the reference period Results: Community malaria prevalence declined from 35% (95% CI: 31, 39) in the 1990s to 2% (95% CI: 1, 4; p