ABSTRACT Background: Malaria in pregnancy increases the risk of anemia, stillbirths, spontaneous abortion, premature delivery and low birth weight. Despite preventive measures put in place, rates of malaria in pregnancy and poor birth outcomes remain persistently high in many parts of Africa. This study was aimed at determining the prevalence of malaria and identifying associated factors in pregnant women attending ANC in Kiryandongo general Hospital. Methods: A total of 185 pregnant women who had attended ANC within 1 year prior to the study who were tested for malaria were enrolled using simple random sampling. Demographic information, obstetric characteristics and malaria prevention practices were obtained using a structured questionnaire. Chi square test and logistic regression analysis using IBM SPSS version 25 were used to compare factors associated with malaria in the pregnant women. Results: The prevalence of malaria from the 185 pregnant women in this study was 5.4%. Participants who did not take IPT were 4 times more likely to have malaria than those who had taken IPT (OR=3.69; 95%CI= 1.062-12.872) and this was significantly associated with malaria infection (p=0.040). Participants who were living in rural areas were five times at risk of having malaria than those in urban areas (OR=4.62; 95%CI=0.577-37.007). Similarly, women who were house wives were 5 times more likely to have malaria (OR=5.18; 95%CI=0.630-42.541) compared to those were employed. Primigravida women had a 2-fold risk of having malaria compared to multigravida women (OR=2.01; 95%CI= 0.587-6.882). Conclusion: Malaria prevalence was low among the pregnant women studied. IPT-sp use was the only factor significantly associated with malaria infection. The use of intermittent preventive treatment and ITNs should be strengthened among all pregnant women. Future research should be conducted in different transmission settings to provide current data on the national prevalence of malaria and risk factors in the context of scaled-up malaria control efforts.