Congenital generalized lipodystrophy (CGL) is a rare autosomal recessive disease that is characterized by loss of subcutaneous and visceral adipose tissues, and associated with dysregulation of glycolipid metabolism. In the present study, we reported the clinical manifestations and treatments of Japanese siblings with CGL caused by BSCL2 gene mutations with a clinical course of approximately 20 yr. Comprehensive management with metreleptin therapy, dietary control with additional medication, and psychosocial counseling in line with the patients’ stages of growth and development were important in achieving long-term metabolic control of this condition.