Transoral stapled diverticulo-esophagostomy (TSDE) has gained increased popularity in surgical treatment of Zenker diverticulum (ZD). One of the advantages of this approach is early rehabilitation with significant decrease in patient morbidity and time to resumption of oral intake as compared with open treatment. The section of the septum between the diverticulum and the esophagus with a flexible endoscopic (ES) approach has also been proposed since mid-90s as an alternative for treatment of ZD. Both these approaches are a minimally invasive approach to treat ZD. We compared the TSDE management of ZD versus the ES treatment in a retrospective consecutive series of patients who were referred to either the ES or surgical unit of our Institute. Fifty-eight consecutive patients underwent treatment for ZD either by TSDE or ES. The two techniques were evaluated for length of hospital stay, diverticulum size, resumption of oral intake, resolution of dysphagia, and complications. Clinical outcome was evaluated throughout a symptom score from 0 to 3, calculated before and after the procedure. The two groups were compared on the various parameters using a Mann–Whitney test. Twenty-eight patients underwent ES and 30 TSDE for ZD. In both groups, a significant decrease in postoperative versus preoperative dysphagia was reported. The average length of hospital stay wasn't significantly different in the two groups (3.38 days for TSDE vs. 2.42 days for ES). The overall complication rate was similar in the two groups. There were two cases in the ES group and three cases in the TDSE group that required an ES revision to take down a residual diverticular wall that produced a mild but persistent dysphagia. Minimally invasive treatment of ZD both with ES and with TSDE is a valuable option for this disease: both techniques are safe and effective, with similar outcome in terms of hospital stay, symptom reduction, and complication rate. Long-term results have to be evaluated.