Transposition of the great arteries (TGA) is the second most common cyanotic congenital cardiac defect and affects around 4.7 in 10,000 live births. Patients present at birth with profound cyanosis due to inadequate oxygen delivery to the systemic circulation. Typical management after birth involves the administration of prostaglandins and oxygen while awaiting surgical repair. Balloon atrial septostomy may be performed depending on the adequacy of the interatrial communication. In this case report, we present a challenging case of TGA ventricular septal defect (VSD) and pulmonary stenosis (PS), demonstrating the importance of bedside clinical examination along with applying basic management principles. The patient underwent a right modified Blalock-Taussig-Thomas shunt (BTT) along with left pulmonary artery (LPA) reconstruction and main pulmonary artery band as an initial palliative procedure. The patient deteriorated postoperatively, with increasing desaturations and oxygen requirements. Though imaging suggested sufficient inter-circulatory mixing, the clinical picture of desaturation without respiratory distress and lack of response to oxygen and pulmonary vasodilatory therapy strongly suggested otherwise. The child therefore underwent a balloon atrial septostomy. Their clinical condition improved and they were discharged three days later. We describe this case's clinical course, medical and surgical management, and learning points.