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Background Transanal endoscopic microsurgery (TEM) has been accepted worldwide for the treatment of local rectal lesions. We aimed to assess the efficacy and safety of TEM in the treatment of rectal neuroendocrine tumors (RNET). Methods A retrospective study of patients who had undergone TEM for RNET at our institution between December 2006 and June 2019 was performed. Demographic and tumor characteristics, operative and pathological details, complications, anal function questionnaires, and follow-up data were included. Results A total of 144 patients was included. TEM was performed as primary excision in 54 patients, after endoscopic forceps biopsy in 57 patients, and after incomplete resection by endoscopic excision in 33 patients. The median size of all primary tumors was 0.6 cm (range, 0.3–2.0 cm), and the negative resection margin was achieved in 142 (98.6%) patients. Postoperative complications (referring to only bleeding) occurred in 3 (2.1%) patients and was successfully managed with conservative method. After a median follow-up of 75.5 months after surgery, 3 patients died of other causes, and 2 patients suffered metastasis. An anal function questionnaire was posted 24 months after TEM. Among the results, 3 (2.1%) patients complained of major low anterior resection syndrome (LARS), including 1 (0.7%) who suffered from complete incontinence, while 6 (4.2%) patients had minor LARS. Conclusions TEM has satisfying long-term outcomes and relatively low anal function disturbance as for the treatment of small RNET. TEM also acts as a preferred salvage treatment for incomplete endoscopic excision.