Pancytopenia in an acutely ill child is commonly a result of bone marrow suppression. Rarely pancytopenia is a manifestation of inappropriate macrophage activation associated with hemophagocytosis. Viral infections account for most cases of secondary hemophagocytosis. We report a case of malaria-associated hemophagocytosis in a child from an endemic area. Systemic parasitic infections should be included in the differential diagnosis of pancytopenia and infection-associated hemophagocytosis. In this rare subgroup of hemophagocytosis, malaria caused by Plasmodium falciparum is the most common parasitic infection.