Malaria continues to pose a significant public health challenge in Africa, particularly in regions where it remains highly endemic. In 2021, approximately half of the global population was at risk of malaria, with an estimated 247 million cases and 619,000 deaths reported worldwide. The African region was disproportionately affected, accounting for 95% of the malaria cases and 96% of the deaths, with children under the age of five comprising 80% of the fatalities. Motivated by these concerns, this study aimed to assess the prevalence and identify factors associated with malaria among children aged 6 to 59 months who presented with fever between October 2023 and January 2024 at five selected health centers in Rubavu District, Rwanda. Using a cross-sectional design, children were tested for malaria through rapid diagnostic tests (RDT) and microscopy. Quantitative data on socio-demographic characteristics and associated factors were analyzed using descriptive statistics and logistic regression. The overall prevalence of malaria among the children was found to be 7.7%. The risk of malaria infection was significantly higher among children aged 24–35 months (adjusted odds ratio [aOR] = 2.823; 95% confidence interval [CI]: 0.330-24.138; p < 0.001) and those from larger families of 3-6 members (aOR = 9.662; 95% CI: 1.264-73.835; p < 0.001). Additionally, children whose mothers or caregivers had only completed primary education were more likely to contract malaria (aOR = 0.914; 95% CI: 0.305-2.741; p < 0.05), as were children from households where the head of the family lacked any formal education (aOR = 0.79; 95% CI: 0.64-0.97; p < 0.001). These findings indicate that age, family size, and the educational level of mothers or caregivers are significant predictors of malaria risk among children under five in Rubavu District, Rwanda. The study underscores the need for targeted interventions that address these demographic and socioeconomic factors to reduce malaria prevalence in this vulnerable population.