Background Various techniques have been described for endoscopic resection of large symptomatic colon lipomas. Lipoma unroofing might provide a safer, more time efficient and easier technique compared to dissection-based techniques, endoscopic mucosal resection (EMR) or loop-assisted resection. The aim of this systematic review was to compare efficacy and safety (endoscopic resolution rates, clinical remission rates and adverse events) of lipoma unroofing with respect to dissection-based techniques, EMR or loop-assisted resection. Methods As most outcomes were binary in nature and several outcomes did not occur in some studies, routine calculation of standard errors in outcome probability was not possible. Therefore, original patient data were extracted, after which efficacy and safety were compared. Results Twenty four studies met the selection criteria, which encompassed 77 lesions (46.8% female, mean age 63 years (interquartile range (IQR) 53–72 years), mean size 45.4 mm (IQR 30.0–60.0 mm). Ten patients underwent unroofing (13.0%), whereas 7 (9.1%), 31 (40.3%) and 29 patients (37.7%) underwent dissection-based techniques, EMR and loop-assisted-snare resection, respectively. Endoscopic resolution rates were 60%, 100% ( p = 0.103), 93.6% ( p = 0.024) and 93.1% ( p = 0.028). Clinical remission rates were identical in all four groups (100%). Amongst patients who underwent EMR and loop-assisted techniques, adverse events were identified in 12.9% ( p = 0.556) and 13.8% ( p = 0.556), respectively, compared to none in the unroofing and dissection-based resection group. Conclusions In patients with large colon lipomas, endoscopic treatment by unroofing, dissection-based resection, EMR and loop-assisted resection provided similar clinical remission rates. Amongst patients undergoing EMR and loop-assisted resection, increased endoscopic resolution rates were seen at the expense of more adverse events, although the latter did not reach statistical significance. Until more reliable comparative data are available, the most optimal resection technique should rely on local expertise and patient profile.