We describe a baby girl with isolate absence of the right pulmonary artery. She had tachypnea just after birth. Several examinations showed absence of the right pulmonary artery and an aortopulmonary collateral artery. After follow-up, cardiac catheterization was performed the age of 14 months. It showed mild pulmonary artery hypertension. The posterior wall of right pulmonary artery was reconstructed with U-shaped in situ pulmonary artery flap and the anterior wall was reconstructed with autologous pericardium patch. Enhanced computed tomography was performed on postoperative day 9 showed occlusion of the right pulmonary artery by a thrombus. Emergency catheterization and thrombolytic therapy was performed with no success. Then, we successfully performed thrombectomy by open surgery. Cardiac catheterization performed at 6 months after the operation showed patency of the right pulmonary artery and improvement of pulmonary artery hypertension.