Abstract Background Endoscopic papillectomy (EP) is considered a relatively safe and minimally invasive treatment for papillary adenomas. In the literature a significant risk for local recurrence is described. The aim of this study was to evaluate long-term recurrence rates and time-to-recurrence. Additionally, risk factors for recurrence, malignancy and adverse events were studied. Methods This is a retrospective study in consecutive patients with papillary adenomas who underwent EP in two tertiary referral hospitals between 2001 and 2018. Primary outcome was recurrence in patients with at least 1-year endoscopic follow-up. Secondary outcomes were surgery free survival, adverse events, and mortality within 30 days after the index procedure. Results A total of 259 patients were found eligible [median age 66 years, 130 male (50.2%)]. Forty-three patients were known with familial adenomatous polyposis (FAP) (16.6%). At least 1-year endoscopic follow-up was available in 154 patients with a total follow-up of 586 person-years and median of 40 months [interquartile range (IQR) 25–75]. Recurrence occurred in 24 cases (15.6%) of which 8 were known with FAP, leading to a recurrence incidence rate of 4.1 per 100 person-years with a median time-to-recurrence of 29 months (IQR 14.75–59.5). Fifty-three patients underwent at least 5-year follow-up, in 6 (11.3%) of them recurrence was encountered after 5 years of which four were known with FAP. No risk factors for recurrence could be identified. Adverse events occurred in 50/259 patients (19.3%). One patient died within 30 days after the procedure. Papillary stenosis occurred in 19/259 (7.3%) of the patients. There were no cases of malignant degeneration during follow-up. Conclusions Recurrence after EP occurs in a significant proportion of patients and occurs even 5 years after EP. This emphasizes the need for long-term follow-up. We advise to consider at least 5-year follow-up in case of a sporadic adenoma, unless comorbidity makes follow-up clinically irrelevant.