Ventricular-assist device therapy for small patients with congenital heart disease is challenging due to its complex anatomy and hemodynamics. We describe a 3-year-old patient with heart failure with truncus arteriosus in the palliative stage. The patient underwent palliative right ventricular outflow tract reconstruction following bilateral pulmonary artery banding. At 6 months of age, the patient developed severe truncal valve regurgitation and left ventricular dysfunction. Emergent truncal valve replacement with a mechanical valve was performed, but left ventricular dysfunction persisted. At 3 years of age, the patient developed acute progression of heart failure triggered by influenza infection. The patient was intubated and transferred to our center to determine the indication for heart transplantation. On the second day after admission, signs of multiorgan failure appeared. Emergent ventricular-assist device implantation for both ventricles was performed with truncal valve closure, ventricular septal defect closure, atrial septal defect closure, and re-right ventricular outflow tract reconstruction. The right ventricular-assist device was successfully removed on the seventh postoperative day. Due to the small pulmonary arteries, severe pulmonary stenosis persisted after ventricular-assist device implantation, but it gradually improved with multiple pulmonary angioplasties. The patient was registered in the Japanese organ transplant network and is awaiting a donor organ in a stable condition.