A congenital fistula between the right pulmonary artery (RPA) and left atrium (LA) is a rare condition that results in central cyanosis. An 11-year-old boy was admitted with exertional dyspnea and easy fatigability. He had severe cyanosis of the lips and limbs with clubbing of the fingers. Systemic oxygen saturation was 70%. There was no abnormal finding on electrocardiography, chest radiography, and echocardiography. Agitated saline injection showed early appearance of contrast bubbles in the LA. A pulmonary arteriovenous fistula was suspected and diagnostic cardiac catheterization was performed. Angiography demonstrated a large fistula between the proximal RPA and LA. The narrowest part of the fistula was 13.8 mm in balloon sizing. A 14-mm Amplatzer septal occluder was deployed at the narrowest site; however, the device migrated to the LA and then to the aortic arch. The device was removed and was successfully reimplanted to the fistula. After the procedure, arterial oxygen saturation increased from 70% to 96% and control angiography demonstrated complete occlusion of the fistula. The patient was symptom-free on follow-up evaluations at 6, 12, and 18 months, with a mean oxygen saturation of 96%. This case represents the first pediatric patient in whom a septal occluder was used.