Background <p>Malaria remains a significant public health concern, particularly in Africa, where children under 5&#xa0;years of age are affected. While mosquito bites are the primary transmission route, congenital malaria caused by transplacental or perinatal transmission can also occur. This case report highlights the challenges in diagnosing congenital malaria and emphasizes the importance of considering it in neonates, especially those born in or with a travel history to endemic areas.</p> Case presentation <p>We report a case of congenital malaria in a 48&#xa0;h-old male neonate born to a 23&#xa0;year-old Ethiopian primigravida. The mother, who had received antenatal care in a nonendemic area, was diagnosed and treated for uncomplicated <i>Plasmodium falciparum</i> malaria with artemether-lumefantrine (Coartem^®) one week before delivery. The delivery occurred at a hospital in a malaria-endemic zone. The neonate presented with respiratory distress and persistent fever, initially managed as early-onset neonatal sepsis. However, blood film microscopy confirmed parasitemia with coinfection of <i>P. falciparum</i> and <i>P. vivax</i>, with a parasite density of 1120&#xa0;parasites/μL. The mother was asymptomatic at the time of the neonate’s diagnosis and tested negative for malaria by both Rapid Diagnostic Test (RDT) and microscopy. The neonate was successfully treated with intravenous artesunate followed by oral artemisinin-lumefantrine, with complete clinical recovery.</p> Conclusion <p>Despite the nonspecific symptoms, this case emphasizes the importance of considering congenital malaria in neonates, particularly those with a history of travel to endemic areas. Blood film microscopy confirmed coinfection and guided effective antimalarial therapy. Strengthening antenatal care services, including intermittent preventive treatment during pregnancy, is recommended to reduce the burden of congenital malaria.</p>