The purpose of this report was to describe the first known case of ileoanal pouch salvage by a low-dose regimen of vinblastine and methotrexate chemotherapy for the treatment of desmoid tumor arising from the mesentery of the ileoanal pouch in a patient who had undergone ileal pouch-anal anastomosis for familial adenomatous polyposis. Mesenteric desmoid tumor involving the ileoanal pouch in a 28-year-old female was treated with vinblastine and methotrexate biweekly for 12 months and monthly for 12 months in an outpatient unit. The desmoid tumor response to the treatment was assessed at routine intervals by physical examination and magnetic resonance imaging. Desmoid tumor was successfully treated with a low-dose regimen of vinblastine and methotrexate chemotherapy without significant side effects, and function of the ileoanal pouch was fully preserved. Magnetic resonance imaging showed a decrease in desmoid tumor size and cellularity, and changes consistent with fibrosis. This is a unique case highlighting the possibility of ileoanal pouch salvage by low-dose combination chemotherapy using vinblastine and methotrexate in a familial adenomatous polyposis patient with mesenteric desmoid tumor.