Congenital malaria is a rare disease both in endemic and non-endemic areas. It is seldom suspected due to its rarity and the fact that its signs and symptoms may be similar to those with neonatal sepsis. Furthermore, clues such as a history of maternal travel to an endemic area during pregnancy or any malaria symptoms may not always be revealed. The situation is further complicated by subjective smear tests and an expensive rapid diagnostic test, especially in developing countries where affordability is an issue. We call attention to the need to consider the diagnosis of malaria in neonates who present with signs and symptoms often confused with sepsis, to enable a quick diagnosis and treatment in order to reduce mortality.