We investigated the relationship between malaria infection and iron status in 531 pregnant women in South Kivu, Democratic Republic of the Congo. Sociodemographic data, information on morbidity, and clinical data were collected. A blood sample was collected at the first antenatal visit to diagnose malaria and measure serum ferritin (SF), soluble transferrin receptor, C-reactive protein, and α1-acid-glycoprotein. Malaria prevalence was 7.5%. Median (interquartile range) SF (adjusted for inflammation) was significantly higher in malaria-infected (82.9 μg/L [56.3-130.4]) than in non-infected (39.8 μg/L [23.6-60.8]) women (P < 0.001). Similarly, estimated mean body iron store was higher in malaria-infected women (P < 0.001). Malaria was significantly and independently associated with high levels of SF. Efforts to improve malaria prevention while correcting iron deficiency and anemia during pregnancy are warranted.