Neonatal malaria may be overlooked likely due to its non-specific features and low prevalence in Malaysia. In this case report, we detail a case of neonatal malaria in an 18-day old baby girl of Myanmar origin who presented with 6 days of intermittent fever but was otherwise well. Initially, she was treated as neonatal sepsis. She then developed thrombocytopaenia and severe anaemia with persistent spikes of temperature. This prompted a series of investigations and multiple changes of antibiotics. The diagnosis of neonatal malaria surfaced when her peripheral blood film incidentally revealed the presence of Plasmodium vivax parasites. Peripheral blood smears are simple and inexpensive. Therefore practising especially in endemic areas for malaria, we need to consider this diagnosis when dealing with neonatal sepsis that does not respond to standard treatment.