Allogeneic hematopoietic stem cell transplantation (allo-SCT) is considered the only curative treatment for relapsed or refractory follicular lymphoma (FL), but it has a high treatment-related mortality rate. Only a few reports, however, have described the efficacy of allo-SCT for FL in the Japanese population. We retrospectively analyzed the outcome of allo-SCT in 30 patients with FL. Seventeen (56.7 %) patients were chemorefractory, whereas 13 (43.3 %) were chemosensitive. An estimated 2-year overall survival rate (OS) and relapse rate of all patients was 46.7 and 20.0 %, respectively. There were no significant differences in the estimated 2-year OS rate between patients who received myeloablative conditioning and those who received reduced-intensity conditioning (P = 0.98), and among the recipients of related bone marrow (BM)/peripheral blood stem cell, unrelated BM and umbilical cord blood (P = 0.20). In patients who were either chemosensitive or chemorefractory at allo-SCT, the 2-year OS rate was 69.2 and 29.4 % (P = 0.06). Patients with mild-to-moderate acute GVHD had better 2-year PFS rate compared with patients who had severe acute GVHD (P = 0.01), but not better PFS compared with patients who had no acute GVHD (P = 0.12). Our results suggest that the graft-versus-lymphoma effects of allo-SCT may provide survival benefits even in patients with chemorefractory FL.