We report a patient who developed orbital MALT lymphoma after autologous peripheral blood stem cell transplantation for follicular lymphoma as relapse of diffuse large B-cell lymphoma. A 54-year-old woman with systemic lymphadenopathy was diagnosed with diffuse large B-cell lymphoma by left supraclavicular lymph node biopsy, and underwent 6 courses of R-CHOP chemotherapy with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone, leading to complete response. Five years later in the follow-up, an abdominal mass with abnormal uptake was found by whole-body 2-[¹⁸F]fluoro-2-deoxy-D-glucose positron emission tomography, and computed tomography-guided biopsy demonstrated follicular lymphoma. She underwent 4 courses of R-IDEA chemotherapy with rituximab, ifosfamide, dexamethasone, etoposide, and cytarabine, resulting in partial response, and then, underwent autologous peripheral blood stem cell transplantation with myeloablative conditioning with R-MCEC chemotherapy (rituximab, ranimustine, cyclophosphamide, etoposide, and carboplatin). She was well for the following 3 years with no treatment until the development of a right orbital mass. The excisional biopsy this time revealed MALT lymphoma. She underwent 3 courses with rituximab monotherapy and local orbital radiation at the total dose of 30 Gy. She had no relapse for the following three years. Relapse as MALT lymphoma after hematopoietic stem cell transplantation for relapsed and refractory lymphoma may not be a poor prognostic sign.