Transposition of the great arteries (TGA) with a rare form of ventricular septal defect (VSD) needs careful attention when choosing the optimal strategy for repair. A neonate with TGA and an atypical VSD, which extended from the perimembranous to the juxta-arterial regions, underwent the arterial switch procedure. The large VSD was successfully closed via a trans-tricuspid combined with a trans-aortic valve approach concomitantly with the arterial switch maneuver. Surgeons need to be aware aware that the types of VSD are diverse in TGA.