Introduction Endoscopic resection for the treatment of gastrointestinal neuroendocrine tumors has a risk of resection margin residues. The related risk factors and prognosis of post-endoscopic resection margin residues have not been fully evaluated. Aim To investigate the associated risk factors and prognostic impact of resection margin residues after endoscopic resection of gastrointestinal neuroendocrine tumors. Material and methods We conducted a retrospective analysis of 129 patients who underwent endoscopic resection for the treatment of gastrointestinal neuroendocrine tumors. Sex, age, location, diameter of tumor, depth of invasion, endoscopic treatment methods, endoscopic ultrasonography (EUS) evaluation, and the work experience of endoscopists were evaluated as potential risk factors. In addition, the prognoses of patients with positive resection margins were analyzed. Results A total of 18 (18/129, 14.0%) patients exhibited positive resection margins after endoscopic resection. Among 16 successfully followed-up patients, 1 died due to rupture of pulmonary artery aneurysms, 2 underwent supplementary surgical operations, and 2 underwent additional endoscopic submucosal dissection. The remaining 11 patients were periodically followed up, and no recurrences were found. The results of univariate analysis suggested that endoscopic treatment method, the depth of invasion, and EUS evaluation correlated with positive resection margin. Multivariate regression analysis suggested that the depth of invasion and EUS evaluation were risk factors for resection margin residues. Conclusions The depth of invasion and EUS evaluation are independent risk factors for positive resection margins after endoscopic resection. This finding suggests that a greater depth of invasion increases the risk for positive resection margins, while EUS evaluation before resection decreases this risk.