The Fontan type operation is currently considered to be a safe procedure. However, in some patients excluded from the indication for the Fontan type operation is contraindicated. A 12-year-old girl given a diagnosis of pulmonary atresia with intact ventricular septum was considered a high risk and was excluded form the indications of the Fontan procedure. She underwent balloon angioplasty for aortic stenosis (valvular) at the age of 2, and bidirectional Glenn anastomosis and aortic valve plasty at the age of 5. At the age of 7, she underwent cardiac catheterization. Although the Fontan procedure was contraindicated, her symptoms gradually progressed year by year, and desaturation caused a decrease in her exercise tolerance. At age 12, she underwent coil embolization of aortopulmonary collaterals and a fenestrated Fontan procedure. In order to keep the procedure as minimally invasive as possible, we performed intraoperative stenting of the peripheral pulmonary stenosis, and all manipulation of fenestrated extracardiac conduit Fontan procedures were performed in the beating heart with cardiopulmonary bypass. The postoperative course was uneventful. The oxygen saturation increased to 95%, and her exercise tolerance dramatically improved. Here we report some special techniques that hybrid operation and satisfactory results.