Eisenmenger syndrome is a severe form of pulmonary arterial hypertension related to congenital cardiac defects. Many patients die at a young age from such complications. The treatment of primary pulmonary hypertension is being applied to Eisenmenger syndrome such as endothelin receptor antagonists, phosphodiesterase-5 blockers, and prostacyclin. We experienced a case of 29-year female with ventricular septal defect-related Eisenmenger syndrome complicated with Down syndrome and Moyamoya disease, who was admitted to intensive care unit due to enteritis-associated septic shock. After the combination treatment with iloprost and sildenafil within the intensive care unit, the patient was able to wean mechanical ventilation without further applications of invasive rescue therapy such as extracorporeal membrane oxygenator. She was later discharged with bosentan. She maintained bosentan therapy for 34 months continuously without aggravations of symptom but eventually died with intracranial hemorrhage, a complication of Moyamoya disease. To our knowledge, this is the first case report of Eisenmenger syndrome accompanied by mosaic Down syndrome and Moyamoya disease.