Background Both endoscopic techniques and transanal surgery are viable options that allow organ preservation for early rectal neoplasms. Whilst endoscopic approaches are less invasive and carry less morbidity, it is unclear whether they are as oncologically effective. Aim To compare endoscopic techniques with transanal surgery in the management of early rectal neoplasms. Methods A systematic literature search was performed for randomised and observational studies comparing these techniques. The pre-specified main outcomes measured were en bloc and R0 resection rates and recurrence. Pair-wise meta-analysis was performed. Results This review included 1044 patients. Transanal surgery had increased R0 resection rates (odds ratio (OR) 2.66; 95% CI 1.64; 4.31; p < 0.001) versus endoscopic management. The latter was associated with higher rates of incomplete resection (OR 2.25; 95% CI 1.14, 4.46; p = 0.02) and further intervention (OR 1.78; 95% CI 1.09, 2.88; p = 0.02). There was no difference in the rates of late recurrence (OR 1.01; 95% CI 0.53, 1.91; p = 0.99) or further major surgery (OR 0.87; 95% CI 0.39, 1.94; p = 0.73) between the groups. Endoscopic treatment was associated with a shorter operating time (weighted mean difference (WMD) − 12.08; 95% CI − 18.97, − 5.19; p < 0.001) and LOS (WMD − 1.94; 95% CI − 2.43, − 1.44; p < 0.001), as well as lower rates of urinary retention post-operatively (OR 0.12; 95% CI 0.02, 0.63; p = 0.01). Conclusion Endoscopic techniques should be favoured in the setting of benign early rectal neoplasms given their decreased morbidity and increased cost-effectiveness. However, where malignancy is suspected transanal surgery should be the preferred option given the superior R0 resection rate.