We report a case of hypoplastic left heart syndrome associated with restrictive interatrial communication and partial anomalous pulmonary venous connection via a right lower pulmonary vein draining to the inferior vena cava. We found unequal pulmonary artery pressure and different pulmonary artery structure, with the right pulmonary artery being lower in pressure and more tortuous and dilated in its peripheral branches than the left. This was attributed to the variant degrees of pulmonary venous obstruction. The left pulmonary venous return was severely obstructed by the restrictive interatrial communication, whereas the anomalous right lower pulmonary vein drained into the inferior vena cava, with less obstruction. To the best of our knowledge, there has never before been a report of differential pulmonary flow associated with a partial anomalous pulmonary vein, in a case of hypoplastic left heart syndrome.