Severe malaria in neonates is a rare occurrence because of the protective effect of fetal haemoglobin and passively acquired maternal antibodies. Despite this protection, severe malaria can still occur and may be confused with neonatal sepsis due to an overlap of clinical manifestations. Therefore, febrile neonates in malaria endemic region should be routinely screened for malaria because any delay in making a diagnosis and instituting adequate and effective treatment can lead to the death of the neonate. This is the first clinical report and successful use of parenteral artesunate for treatment of severe malaria in a Nigerian neonate that is documented in literature to the best of our knowledge.