We report five patients with acute leukemia who underwent allogeneic hematopoietic stem cell transplantation (HSCT) following surgical resection of pulmonary aspergillosis. The patients were three men and two women with a median age of 40 (range, 32 approximately 60). The diagnosis, based on CT imaging, Aspergillus antigen, culture, and histopathology of resected lung specimens, included two proven and three possible pulmonary aspergillosis. Median duration from surgery to HSCT was 2.5 months (range, 1.0 approximately 20). Pre-transplant restrictive-type lung dysfunction was observed in four patients. Antifungal prophylaxis after HSCT was attempted with voriconazole in three patients, amphotericin-B in one patient, and micafungin in one patient. No patients experienced a relapse of pulmonary aspergillosis, although three patients died after HSCT. The causes of death included leukemia relapse in two and hemophagocytic syndrome in one. These results suggest that pre-transplant surgical resection with post-transplant prophylactic antifungal agents seems to be an effective strategy to prevent the relapse of pulmonary aspergillosis in patients with residual disease in the lung before allogeneic HSCT.