Children below five years of age account for about 80% of malaria deaths globally. As malaria continues to decline in many parts of sub-Saharan Africa and malaria rapid diagnostic tests become increasingly used, it is crucial to evaluate the critical outcomes from innovative strategies involving community health workers (CHWs) and local health facilities in fever management accounting for the spatial and temporal heterogeneity in infection risk. This study aimed to determine the proportion of fever cases due to malaria and non-malarial infections in space and time among children below five years of age and their relationship with rainfall in Siaya County in Kenya. A prospective longitudinal incidence study of all children tested for malaria by CHWs, and in health facilities were conducted between January 2013 and December 2015. The incidence proportion of malaria cases reported by CHWs increased with time, and the difference over the years was statistically significant (P<0.001). At health facilities, the incidence proportion of malaria cases decreased with time though the difference between the years was not statistically significant (P=0.399). For non-malarial cases reported by CHWs, the incidence proportion was lowest in 2014 and highest in 2013, and the difference over the years (2013-2015) was not statistically significant (P>0.001). At the health facilities, the incidence proportion of non-malarial cases was highest in 2014 and lowest in 2015, and the difference between the years (2013-2015) was not statistically different (P>0.001). None of the tested rainfall regimes (current, lagged, or cumulative) were associated with malaria and non-malarial cases (P>0.1). Five villages (Ramula, Marenyo, Uranga, Bongo, and Lihanda) had a significantly higher incidence proportion of malaria cases (P<0.05), while all villages except Nyawara, Marenyo, and Nyandiwa had a significantly higher incidence proportion of non-malarial cases (P<0.05). CHWs have the potential to play a role in the management of fever-related illnesses. The risk of diagnosing malaria seems predictable, while non-malarial cases occur throughout the year. These findings present opportunities for preparedness and policy actions to scale-up community health services.

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