A 54-year-old male was diagnosed with follicular lymphoma in September 2003. Despite multiple chemotherapies, including autologous hematopoietic stem cell transplantation (HSCT) with high-dose chemotherapy, the disease eventually relapsed. Additionally, bone marrow analysis revealed the co-emergence of therapy-related myelodysplastic syndrome (t-MDS) in February 2012. In March 2012, we performed related allogeneic HSCT for the treatment of both malignancies. This strategy was successful and the patient has remained free from both malignancies for 23 months. Allogeneic HSCT is a potent curative therapeutic option for both t-MDS and refractory follicular lymphoma.