Congenital malaria (CM) has been considered to be rare, even in malaria-endemic areas but the disease can result in significant neonatal morbidity. Because of its rarity, the disease may go undiagnosed for a prolonged period in a seriously ill infant. We report the first case of Plasmodium malariae CM from a HIV mother. HIV could have facilitated the transfer of erythrocytic persistent P. malariae through the placenta to the fetus.