Background: While a shift to minimally invasive techniques in rectal cancer surgery has occurred, non-inferiority of laparoscopy in terms of oncological outcomes has not been definitely demonstrated. Transanal total mesorectal excision (TaTME) has been pioneered to potentially overcome difficulties experienced when operating with a pure abdominal approach deep down in the pelvis. This study aimed to compare short-term oncological results of TaTME versus laparoscopic TME (lapTME), based on a strict anatomical definition for low rectal cancer on MRI. Methods: From June 2013, all consecutive TaTME cases were included and compared to lapTME in a single institution. Propensity score-matching was performed for nine relevant factors. Primary outcome was resection margin involvement (R1), secondary outcomes included intra- and post-operative outcomes. Results: After matching, forty-one patients were included in each group; no significant differences were observed in patient and tumor characteristics. The resection margin was involved in 5 cases (12.2%) in the laparoscopic group, versus 2 (4.9%) TaTME cases (P = 0.432). The TME specimen quality was complete in 84.0% of the laparoscopic cases and in 92.7% of the TaTME cases (P = 0.266). Median distance to the circumferential resection margin (CRM) was 5 mm in lapTME and 10 mm in TaTME (P = 0.065). Significantly more conversions took place in the laparoscopic group, 9 (22.0%) compared to none in the TaTME group (P < 0.001). Other clinical outcomes did not show any significant differences between the two groups. Conclusion: This is the first study to compare results of TaTME with lapTME in a highly selected patient group with MRI-defined low rectal tumors. A significant decrease in R1 rate could not be demonstrated, although conversion rate was significantly lower in this TaTME cohort.