Pulmonary alveolar proteinosis (PAP) is a rare disease in children characterized by intra-alveolar accumulation of surfactant proteins, which severely reduces gaseous exchange. Whole lung lavage (WLL) is the preferred technique for the treatment of severe PAP. Herein, we present a pediatric case of PAP treated with WLL. An 11-year-old boy was admitted with the chief complaint of a dry cough lasting 6 months. He developed symptoms of dyspnea on exertion and had difficulty in climbing stairs. He was ultimately diagnosed with PAP through video-assisted thoracoscopic lung biopsy. As first-line of treatment for PAP, he underwent therapeutic WLL for each of his lungs on separate days. After a brief recovery, his symptoms gradually worsened; therefore, he underwent a second WLL. This is the first pediatric case of PAP relapse despite successful WLL in Korea.