We report a case of transposition of the great arteries (TGA) with severe pulmonary hypertension from the right to left shunt in the right modified Blalock-Taussig shunt. The patient was diagnosed with TGA with a small ventricular septal defect, restrictive patent foramen ovale, and patent ductus arteriosus. Balloon atrial septostomy was performed, and an arterial switch operation (ASO) was planned. However, ASO was delayed during the neonatal period due to cerebral bleeding. Moreover, left outflow tract obstruction was noted ; hence, the surgical strategy was shifted to an atrial switch operation or Rastelli type operation. The patient was palliated at the age of 5 months with a right 4-mm Gore-Tex modified Blalock-Taussig shunt. After this procedure, he was followed up at the outpatient clinic with good saturation level. However, at 9 months, he revisited the hospital due to septic shock. His SpO2 was 60% in the upper right limbs and 40% in the upper left and lower limbs. Nitric oxide inhalation and 100% oxygen were administered to improve pulmonary hypertension and subsequent differential cyanosis. Pulmonary hypertension decreased from over-systemic to 70% of the systemic arterial pressure. The Senning procedure with a fenestration in an atrial baffle was successfully performed at the age of 1 year.