Ileal pouch‐anal anastomosis (IPAA) after total proctocolectomy (TPC) can be conducted with either hand‐sewn or stapled anastomosis for patients with familial adenomatous polyposis (FAP). Although stapled IPAA without mucosectomy has a higher risk for developing adenomas in the remnant mucosa, it is the simpler procedure with potential benefit in short‐term outcomes. However, it remains controversial as to whether stapled IPAA has any advantages in reducing postoperative complications. The aim of the present study was to compare the postoperative complications and short‐term outcomes of stapled and hand‐sewn IPAA for patients with FAP, using a multicenter cohort sample in Japan. Data of 143 patients with FAP who underwent TPC with stapled IPAA (n=37) and hand‐sewn IPAA (n=106) at 23 institutions between 2000 and 2012 were collected. Postoperative complications, proportion of ostomy, fecal continence and overall survival were compared. Overall rates of the Clavien‐Dindo grade II‐IV complications were not different between the two groups (19% in stapled vs 25% in hand‐sewn, P=.42), with significantly fewer pouch‐related complications including leakage, pelvic abscess, vaginal fistula and anastomotic stricture in stapled IPAA (none in stapled vs 11% in hand‐sewn, P=.036). There was no mortality. Proportion of ostomy at 12 months was similar (2.7% in stapled vs 4.3% in hand‐sewn, P=.26). Mean Wexner score was similar. (0.47 in stapled vs 2.0 in hand‐sewn, P=.12). Five‐year overall survival excluding Stage IV patients was 96% in both groups. Stapled IPAA is a safe option in patients with FAP with a potential benefit in reducing pouch‐related complications.