Chronic graft-versus-host disease (cGVHD) frequently complicates allogeneic hematopoietic stem cell transplantation (HSCT), but small bowel involvement with obstruction is rarely observed. We report two patients who underwent allogeneic sibling HSCT and developed severe cGVHD involving the small bowel, causing unremitting obstructive symptoms and malnutrition despite maximal immunosuppression. Both patients underwent ileal resection and stricturoplasties. The first patient promptly improved, and remains asymptomatic 32 months after transplant. Three weeks after the resection of 90 cm of small bowel, the second patient developed leaking stricturoplasty and peritonitis, with a relapse of chronic myelogenous leukemia in accelerated phase. Later, an enterocutaneous fistula required additional small bowel resection and ileostomy. The patient subsequently died from pulmonary infection a few weeks after the last surgical procedure. Similar to inflammatory bowel disease, these two cases highlight that surgery may be a valuable option in patients who present with obstructive severe cGVHD refractory to aggressive immunosuppression.