Branch pulmonary artery stenosis may occur in 4%-28% of patients after an arterial switch operation. Balloon dilation can be attempted with variable results, while stenting is a more definitive option when balloon dilation fails. We report the case of a young boy who underwent balloon dilation of a stenosed left pulmonary artery 9 years after an arterial switch operation and was noted to have an aortopulmonary window about a year later. This was treated with covered stent implantation, which dealt both with the aortopulmonary window and the residual stenosis. The diagnostic process with cardiac magnetic resonance imaging and cardiac catheterization of such an unusual entity as well as the transcatheter management are discussed in detail.