Background: Kenya has a lower malaria incidence in comparison to other African malaria-endemic nations. Malaria is a significant public health concern in the country. The malaria indicator survey (MIS) data were analyzed using the logistic regression model. Nonetheless, independent data may be the cause of most MIS's hierarchical structure. This approach does not consider any association between data points within a cluster, as it assumes that the individual malaria statuses are independent of their causes. The approach may lead to biased analysis conclusions. The primary goal of this research is to determine the impact of sample enumeration areas (SEAs) and SEA features on individual malaria rapid diagnostic test (RDT) results. We are interested in identifying key factors influencing household members' malaria RDT findings or Kenya's malaria prevalence and assessing variation. Methods: Our study utilized the robust 2020 Kenya National Malaria Indicator Surveys (KMIS) dataset, which is representative of the entire nation. This dataset, comprising 301 clusters (134 urban and 167 rural areas), was instrumental in applying several multilevel models, including random sample and sample Enumeration Area (SEA) effects. We also considered the weights used in the s survey design, which is used to adjust uneven probabilities of choice within clusters, further enhancing the reliability and relevance of our findings. The methods used in this study involved a rigorous analysis of the KMIS dataset, including applying multilevel models and considering survey design weights to ensure the robustness and strength of our results. ResultsThis study's findings are significant and crucial in understanding the prevalence of malaria in Kenya. The findings reveal that factors such as region, place of residence, mosquito bed net use, water source location, wealth index, age, household size, and altitude are significantly associated with malaria's prevalence.After accounting for these variables, systematic changes across SEAs accounted for approximately 47.1% of the remaining variability in malaria occurrence in the study locations. In contrast, the remaining 52.9% was projected to be unmeasured differences between individuals or family units. These findings provide a detailed explanation of the various processes that influence malaria prevalence in Kenya. Conclusions: The study's multilevel logistic regression model, which includes random effects, identified two SEA-level and eight individual/household risk factors for malaria infection. Thus, increasing the availability of insecticide-treated bed nets is one crucial element that public health policymakers should consider. Furthermore, health planners can organize spatially targeted initiatives to prevent malaria transmission with the help of spatial clustering data.