This study primarily aimed to compare the long-term prognosis of patients who underwent total colectomy/proctocolectomy with or without mucosectomy to the dentate line for the diagnosis of familial adenomatous polyposis (FAP). Patients who underwent total colectomy/proctocolectomy for FAP between January 1979 and December 2020 and were followed up at Hamamatsu University Hospital were included in this study. Those who underwent total proctocolectomy with hand-sewn ileal pouch-anal anastomosis were defined as the mucosectomy group. Those who underwent total colectomy or total proctocolectomy using the stapled ileal pouch-anal anastomosis approach were defined as the no mucosectomy group. A total of 61 individuals (37 families) were diagnosed during the surveillance period (median, 191months). Between the mucosectomy (n = 24) and no mucosectomy groups (n = 34), metachronous rectal cancer was significantly more common in the no mucosectomy group (21% in no mucosectomy vs. 0% in mucosectomy, P = 0.02). Overall survival in the no mucosectomy group was worse than that in the mucosectomy group (84.5% in no mucosectomy vs. 100% in mucosectomy at 120months, 81.1% vs. 90.0% at 240months, 50.6% vs. 75.0% at 360months, P = 0.09). Cox regression analysis revealed an independent effect of not performing mucosectomy on overall survival (P = 0.03). Long-term surveillance revealed that colectomy or total proctocolectomy without mucosectomy had a negative impact on the overall survival of patients with FAP. Therefore, we recommend total proctocolectomy with mucosectomy, i.e., hand-sewn ileal pouch-anal anastomosis, for FAP.