Globally, malaria remains a major public health problem. In 2019 an estimated 229 million cases of malaria were reported, WHO African region accounted for 94% of total cases. In Kenya, malaria is a leading cause of morbidity and mortality among children under five years living in malaria endemic zones. This study investigated the factors that are associated with malaria prevalence among children under-five years living in North West Kisumu Ward, Kisumu County. This cross-sectional study was carried out at Chulaimbo County Hospital from July 2019 to January 2020. Using a validated structured questionnaire, data were obtained from 369 randomly sampled children < 5 years who presented with signs and symptoms of malaria and had malaria positive or negative test results from the laboratory. Children with chronic illnesses such as HIV were not enrolled. Chi-square test of independence and logistic regression analysis was done using SPSS 20.0 software. Out of 369 participants, 183 (49.6%) tested positive for malaria. Child age was significantly associated with malaria (P = 0.04). There were low malaria odds among females (OR = 0.92, 95% CI 0.61-1.39) and in households where mothers (OR = 0.47, 95% CI 0.16-1.37) or fathers (OR =0.86, 95% CI 0.31-2.35) had university education. Low malaria risk was also reported among children whose fathers had employment (OR = 0.94,95% CI 0.49-1.80). On the contrary, high malaria risk was recorded among children whose mothers were employed (OR = 1.24, 95% CI 0.62-2.50). Children from married respondents were likely to test positive for malaria (OR = 1.07, 95% CI 0.60-1.93). Children who used bed nets were less likely to test positive for malaria (OR = 0.70, 95% CI 0.35-1.41). Surprisingly, low malaria risk was reported among severely malnourished children (OR = 0.71, 95% CI 0.42-1.20). Child age and bed net use, but not nutritional status, are important determinants of malaria prevalence in children under 5 years. The Ministry of Health should promote more efforts towards protecting young children from malaria, by ensuring access and use of bed nets, and enhancing health education.