Malaria is caused by protozoa of the genusPlasmodiumand remains a major public health burden in Sub-Saharan Africa. Its prevalence varies between 9 to 18% with harmful consequences to both the mother and her baby, including adverse pregnancy outcomes such low birth weight, high morbidity, and mortality. However, effective antenatal strategies for improving maternal and child health outcomes through the prevention, early detection, and treatment of malaria in pregnancy, are still lacking in resource-constrained settings. Here, we sought to determine the predictors of low birth weight in pregnant women with malaria in a cohort study in Webuye hospital. Prior to the enrollment of 140 participants, permission was sought from relevant institutions and consent from the participants. Malaria test was conducted either with microscopy or rapid test, and then the cohort splits into malaria positive and negative followed up from the first antenatal visit (March 2022) and delivery (December 2022). Before data collection, training, pre-testing and quality control were duly observed. Data were fed into SPSS 27 version, Chi-square and Fischer’s Exact were used for bi-variate analysis at a p-value less or equal 0.05 (95%). Our results revealed that birth cohort with malaria did not result in significant low birth weight with a relative risk of 0.999, confidence level of 0.926-1.077. The prevalence of low birth weight was 4.6% with 6 cases of which 3 (4.5%) in the negative cohort and 3 (4.7%) in the positive cohort. Anemic pregnant women were 41 (31.5%), HIV were 5 (3,8%), pre-eclampsia was 5 (3.8%), gestational diabetes was 2 (1.5%). Confounding factors, such as anemia, HIV, preeclampsia, and gestational diabetes did not influence low birthweight (p-value >0.923). Otherwise, most of the participants were aged 18–25 years, were primigravida, were married, had secondary school level education, earned between 20-30 thousand shillings, were resident in rural areas, and were in their second trimester. Marital status, gestational age and area of residence were associated with malaria with a p-value less than 0.001 and 0.028 respectively.