A 6-year-old boy had previously undergone total anomalous pulmonary venous connection repair and postoperative pulmonary vein stenosis release. Magnetic resonance imaging revealed blood stasis caused by a collision between the inflow from the pulmonary veins and the outflow from the left atrial appendage. A surgical specimen revealed evidence of advanced thrombus attachment. Infra-cardiac total anomalous pulmonary venous connection with an antler appearance may be a risk factor for thrombus formation in the left atrial appendage and for postoperative pulmonary venous stenosis due to blood flow collision in the left atrium after total anomalous pulmonary venous connection repair.