Isolated right superior vena cava (SVC) draining to the left atrium (RSVC-LA) is an extremely rare cyanotic congenital heart disease (CHD). Such lesion is easily missed with improper scanning or inattentive interpretation of echocardiography. This can result in potential systemic severe complications. We report a child with RSVC-LA who has two significant non-cardiac co-morbidities, including Waardenburg syndrome and n neurofibromatosis type I (NF1). This patient was referred to cardiology assessment due to unexplained low saturation and was diagnosed as RSVC-LA; however, fortunately not yet showing complications of systemic thromboembolic phenomenon (STEP).