Sinus of Valsalva aneurysm is a rare disease characterized by the partial elevation of the aortic root. Few reports are available on the surgical treatment for infants. We report the repair of an extremely rare case of a sinus of Valsalva defect with a ventricular septal defect and right ventricular outflow tract stenosis in an infant. It was not a sinus of Valsalva aneurysm, but it exhibited abnormal partial bulging of the aortic root and forming an aneurysm-like cavity within the right ventricular myocardium. We performed direct closure of the sinus of Valsalva aneurysm-like cavities and intracardiac repair in two stages. Three years after total repair, the patient remained healthy and asymptomatic.