Lymphedema is a rare complication of sirolimus treatment in transplantation patients. We present a case of a 14-year-old female patient who developed lymphedema in three extremities. The patient had undergone ileal and colon resections after sustaining a gunshot to her abdomen. Four months after the injury, she had developed a short bowel syndrome and underwent small intestine transplantation from a cadaver and mesenchymal stem cell transplantation to prevent rejection. Because kidney failure developed at postoperative month 3, mycophenolate mofetil therapy was discontinued and sirolimus therapy was initiated. The patient was monitored under this therapy until postoperative month 11 when she had swelling in both the legs and left arm. Her condition significantly improved with complex decongestive therapy. This is the first case in the literature involving mesenchymal stem cell transplantation together with ileum transplantation. This case is also noteworthy in terms of lymphedema treatment administered and the involvement of three extremities.