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Purpose Neuroendocrine tumor is a rare tumor in the rectum, but incidence has been increasing. Local excision is an option for treatment of small tumors, and transanal excision or endoscopic resection can be undergone. But indications for local excision have not been established yet. This study was to compare the long-term oncologic outcomes between transanal excision and endoscopic resection for rectal neuroendocrine tumor. Methods Patients diagnosed and treated with rectal neuroendocrine tumor from 2000 to 2015 were collected prospectively, and medical records were analyzed retrospectively. Results Forty patients were included, mean age was 50.20±13.35 years (male:female=23:17). Transanal excision and endoscopic resection were performed in 28 (70%) and 12 (30%) patients, respectively. Mean tumor size was 0.63±0.37 cm, and tumor location was 5.45±1.89 cm from anal verge. Tumor location was more distal rectum in transanal excision (5.04±1.73 cm vs. 6.42±1.98 cm, P=0.049). Pathologic T stage was T1 in all patients. Most of the patients (90%) showed tumor grade 1. After median 24 months (range, 0–86 months) follow-up, one patient (2.5%) experienced local recurrence. The patient underwent further transanal excision. There was no mortality after local excision. Conclusion Local excision is a safe and effective treatment for small-sized neuroendocrine tumors in rectum.