Backgrounds: Although transanal endoscopic surgery is practiced worldwide, there is no consensus on comparative outcomes between transanal endoscopic operation (TEO) and transanal excision (TAE). In this study, we reviewed our experiences with these techniques and compared patients who underwent TEO and TAE using propensity score matching (PSM). Methods: A total of 207 patients underwent local rectal tumor excision between January 2008 and November 2015. To overcome selection bias, we used PSM to achieve a one-to-one TEO: TAE ratio. We included baseline characteristics, age, sex, surgeon, American Society of Anesthesiologists score, tumor location (clockwise direction), involved circumference quadrants, tumor size, and pathology. Results: After PSM, 72 patients were included in each group. The tumor distance from the anal verge was higher in the TEO group (8.0 [5–10] vs. TAE: 4.0 [3–5], p < 0.001). Complication rates did not differ between the groups (TEO: 8.3% vs. TAE: 11.1%, p = 0.39). TEO was associated with a shorter hospital stay (3.01 vs. 4.68 days, p = 0.001), higher negative margin rate (95.8 vs. 86.1%, p = 0.039), and non-fragmented specimen rate vs. TAE (98.6 vs. 90.3%, p = 0.029). Conclusions: TEO was more beneficial for patients with higher rectal tumors. Regardless of tumor location, involved circumference quadrants, and tumor size, TEO may more effectively achieve negative resection margins and non-fragmented specimens. Consequently, although local excision method according to tumor distance may be important, TEO will become the standard for rectal tumors.