BackgroundMalaria risk factors at household level are known to be complex, uncertain, stochastic, nonlinear, and multidimensional. The interplay among these factors, makes targeted interventions, and resource allocation for malaria control challenging. However, few studies have demonstrated malaria’s transmission complexity, control, and integrated modelling, with no available evidence on Uganda’s refugee settlements. Using the 2018–2019 Uganda’s Malaria Indicator Survey (UMIS) data, an alternative Bayesian belief network (BBN) modelling approach was used to analyse, predict, rank and illustrate the conceptual reasoning, and complex causal relationships among the risk factors for malaria infections among children under-five in refugee settlements of Uganda.MethodsIn the UMIS, household level information was obtained using standardized questionnaires, and a total of 675 children under 5 years were tested for malaria. From the dataset, a casefile containing malaria test results, demographic, social-economic and environmental information was created. The casefile was divided into a training (80%, n = 540) and testing (20%, n = 135) datasets. The training dataset was used to develop the BBN model following well established guidelines. The testing dataset was used to evaluate model performance.ResultsModel accuracy was 91.11% with an area under the receiver-operating characteristic curve of 0.95. The model’s spherical payoff was 0.91, with the logarithmic, and quadratic losses of 0.36, and 0.16 respectively, indicating a strong predictive, and classification ability of the model. The probability of refugee children testing positive, and negative for malaria was 48.1% and 51.9% respectively. The top ranked malaria risk factors based on the sensitivity analysis included: (1) age of child; (2) roof materials (i.e., thatch roofs); (3) wall materials (i.e., poles with mud and thatch walls); (4) whether children sleep under insecticide-treated nets; 5) type of toilet facility used (i.e., no toilet facility, and pit latrines with slabs); (6) walk time distance to water sources (between 0 and 10 min); (7) drinking water sources (i.e., open water sources, and piped water on premises).ConclusionRanking, rather than the statistical significance of the malaria risk factors, is crucial as an approach to applied research, as it helps stakeholders determine how to allocate resources for targeted malaria interventions within the constraints of limited funding in the refugee settlements.