Pulmonary alveolar proteinosis is characterized by accumulation of surfactant phospholipids and proteins within alveoli of the lungs. Sequential whole lung lavage is an accepted modality for treatment of pulmonary alveolar proteinosis. Generally, the degree of hypoxemia is tolerable while only one lung is being ventilated and the other is being lavaged. However, one patient became severely hypoxemic when one lung ventilation was performed through the left lung because of R-to-L shunt due to the lung cancer in the left lower lobe. Therefore, whole lung lavage on the right lung was successfully performed, while utilizing venovenous extracorporeal membrane oxygenation.