Congenital cytomegalovirus infection causes lethal diseases with neurological, visual, auditory and systemic injuries, including the hemophagocytic syndrome. Hemophagocytic lymphohistiocytosis (HLH) can be caused by primary hereditary immunological defects, as well as several infectious triggering factors, such as viruses, bacteria and fungus, among them the cytomegalovirus (CMV). Here we present the case report of a male newborn male, delivered by cesarean at term (gestation age of 39 weeks), weighing 3,250 g, with suffusion skin lesions spread throughout the body, anemia, generalized edema, hepatosplenomegaly, thrombocytopenia associated with grunts and difficulty breathing, treated with ganciclovir after receiving the diagnosis of congenital CMV infection. After a few days of hospitalization, the patient presented with high fever, persistent hepatosplenomegaly and pancytopenia, in addition to elevated ferritin and triglycerides, receiving the diagnosis of HLH treated with immunosuppressive therapy, corticosteroids and intravenous human immunoglobulin. The present case report highlights the importance for health professionals to carry out the investigation of congenital diseases, especially in developing countries, as well as their complications, such as HLH.