The presence of thrombocytopenia in cyanotic congenital heart disease (CCHD) is an uncommon, but well-known condition. We present a patient with pulmonary atresia with ventricular septal defect (PA with VSD) requiring a multi-stage operation. We were unsure whether the patient's hypoxia was the cause of his thrombocytopenia, as the hypoxia was relatively mild. His thrombocytopenia improved following reoxygenation after the Rastelli operation (total correction of PA with VSD). From these findings, we suggest that if a patient with CCHD presents with thrombocytopenia without an obvious cause, hypoxia-induced thrombocytopenia should be considered, regardless of the degree of hypoxia, platelet count, or hematocrit percentage.