A 31-year-old man with Crohn's disease in remission after 6-year treatment with infliximab developed nasopharyngeal diffuse large B cell lymphoma. Infliximab was discontinued, and complete remission was achieved following chemotherapy with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone. However, the patient subsequently experienced severely symptomatic Crohn's disease relapse. Therapy with adalimumab was initiated, and the patient attained remission. However, after 3 months, he suffered a recurrence of the lymphoma. Adalimumab was discontinued, and the patient received further chemotherapy (with rituximab, etoposide, cisplatin, methylprednisolone, and high-dose cytarabine) treatment and underwent allogeneic hematopoietic stem cell transplantation. Following the procedure, Crohn's disease and lymphoma have remained in complete remission for 5 years. There are limited reports on Crohn's disease remission after allogeneic hematopoietic stem cell transplantation. Therefore, we present this case report and a review of the existing literature on allogeneic stem cell transplantation for Crohn's disease.