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Abstract Background: Malaria is a leading cause of morbidity and mortality among children under five in Malawi, and especially among those from rural areas of central Malawi. The goal of this study was to examine the prevalence and determinants of malaria infection among children in rural areas of the Dowa district in central Malawi. Methods: A multistage cross-sectional study design was used to systematically sample 523 child‑mother dyads from postnatal clinics. A survey was administered to mothers and a rapid malaria infection diagnostic test was administered to children. The main outcome was positive malaria diagnostic tests in children. Logistic regressions were used to determine risk factors associated with malaria among children aged 2 to 59 months. Results: The prevalence of malaria among children under five years was 35.4%. Results suggest that children of mothers who experienced recent intimate partner violence were more likely to be diagnosed with malaria ( AOR : 1.88, 95% CI : 1.19–2.97; P = 0.007) than children of mothers who did not. Children of mothers who had no formal education were more likely to be diagnosed with malaria ( AOR : 2.77, 95% CI : 1.24–6.19; P = 0.013) than children of mothers who had received secondary education. Children aged 2 to 5 months and 6 to 11 months were less likely to be diagnosed with malaria ( AOR : 0.21, 95% CI : 0.10–0.46; P = 0.000 and AOR : 0.43; 95% CI : 0.22–0.85; P = 0.016, respectively) than children aged 24 to 59 months. Conclusion: We found that the prevalence of malaria infection among children in the study area was comparable to the national level. In addition to available malaria control programs, further attention should be paid to children whose mothers have no formal education, children aged 24 to 59 months and children of mothers that are exposed to IPV in the area.