Background: Bronchiolitis obliterans syndrome (BOS) is a life-threatening respiratory complication of allogeneic hematopoietic stem cell transplant (HSCT). Even though a lung function test is crucial in monitoring BOS, little information exists on the test’s association with prognosis in children with BOS. Objectives: The purpose of this study was to determine the correlation between changes in lung function after BOS diagnosis and long term outcomes. Methods: A total of 428 children received allogeneic HSCT from January 2006 to December 2017 at Asan Medical Center. Twenty-three of those children (5.4%) were diagnosed with BOS after allogeneic HSCT, and their clinical data were reviewed. Twenty-one subjects underwent regular pulmonary function tests for 24 months after the occurrence of BOS. Results: Among the 21 children with BOS, eight died, five underwent a lung transplant (TPL), and 15 required oxygen (O2) therapy. The FEV1% predicted (pred), FVC% pred, and FEF25-75% pred were 37.8±12.7% (mean±SD), 62.2±16.2%, and 16.4±9.6%, respectively, upon BOS diagnosis. Changes in the FEV1% pred were greater in the death and lung TPL group (-24.8±22.3%) than the survival without lung TPL group (5.7±21.8%), and greater in the O2 therapy (-19.4±23.4%) group than the group without O2 therapy (14.2±20.0%) during the first three months after BOS diagnosis. Conclusion: The change of FEV1 during the first three months after BOS correlated with the prognosis including survival, lung transplantation, and O2 therapy. These results suggest more active intervention in the first three months after BOS diagnosis may be needed to improve prognosis.