During one-lung ventilation (OLV) in the lateral position, the dependent, ventilated lung receives more blood flow than the non-dependent, non-ventilated lung owing to gravity, improving the match of ventilation and perfusion. Conversely, in the rare clinical situations when OLV is applied to the non-dependent lung, arterial oxygenation can get worse due to considerable shunt flow to the dependent non-ventilated lung. We report a case of severe hypoxemia during carinal resection under OLV of a non-dependent lung. In this case, OLV had to be applied to the non-dependent lung in the lateral position because the bronchus of the non-dependent lung was anastomosed with the trachea, whereas the bronchus of the dependent lung had already been resected for carinal resection. The subsequent hypoxemia resulting from the shunt flow to the dependent non-ventilated lung was treated successfully by ligating the pulmonary artery of the dependent lung.