Purpose The long-term prognosis of stapled and hand-sewn ileal pouch–anal anastomoses in familial adenomatous polyposis patients in Japan remains unknown. This study aimed to compare the overall survival in familial adenomatous polyposis patients who underwent stapled or hand-sewn ileal pouch–anal anastomosis. Methods This multicenter retrospective study was conducted at 12 institutions in Shizuoka Prefecture, Japan. The clinical outcomes of 53 eligible familial adenomatous polyposis patients who underwent stapled ( n  = 24) and hand-sewn ( n  = 29) ileal pouch–anal anastomosis were compared. Results The median follow-up duration was 171.5 months. The incidence of adenoma in the remnant rectum or anal transitional zone and metachronous rectal cancer was significantly more common in stapled ileal pouch–anal anastomosis (adenoma: stapled, 45.8%, vs. hand-sewn, 10.3%, p  = 0.005; metachronous rectal cancer: 29.2%, vs. none, p  = 0.002). The number of deaths was remarkably higher in stapled ileal pouch–anal anastomosis ( p  = 0.002). Metachronous rectal cancer was the most common cause of death. Overall survival was worse in stapled ileal pouch–anal anastomosis than in hand-sewn ileal pouch–anal anastomosis (120 months, 90.7% vs. 96.6%; 240 months, 63.7% vs. 96.6%; p  = 0.044). Cox regression analysis revealed the independent effects of preoperative advanced colorectal cancer and stapled ileal pouch–anal anastomosis on overall survival. Conclusion Stapled ileal pouch–anal anastomosis negatively affected the overall survival of familial adenomatous polyposis patients. Therefore, hand-sewn ileal pouch–anal anastomosis is recommended for better prognosis in these patients.