OBJECTIVE Endoscopic resection for early gastric cancers that meet the expanded indication is considered to be an investigational treatment. The study aim was to evaluate long-term outcomes of endoscopic resection compared with surgery for early gastric cancers meeting the expanded indication. METHODS We retrospectively reviewed data from patients who underwent endoscopic resection or surgery for gastric cancers meeting the expanded indication between 2001 and 2009. Overall survival rate was the primary outcome; gastric cancer recurrence rates and complication rates were secondary outcomes. RESULTS Among 457 patients included, 165 underwent endoscopic resection and 292 surgery, with median follow-up duration of 58.6 months. The 5-year overall survival rates were 97.5 % and 97.0 % for endoscopic resection and surgery, respectively; Kaplan-Meier analysis showed no significant difference (P = 0.425). The 5-year gastric cancer recurrence rate was higher for endoscopic resection than for surgery (4.8 % vs. 0.3 %; P < 0.001) mainly because of metachronous cancers which developed only in the endoscopic resection group (9/165, 5.5 %). Most of the metachronous cancers (88.9 %) were curatively treated with endoscopic resection. Early complication rates were similar between the groups (P = 0.557), but the endoscopic resection group had more grade III or higher complications according to the Clavien-Dindo classification compared with the surgery group (4.8 % vs. 1.4 %, P = 0.026). Late complications occurred only following surgery (4.8 %, P = 0.004), and most (92.9 %) were grade III or higher. CONCLUSIONS Endoscopic resection may be an optimal alternative to surgery for gastric cancers that meet the expanded indication criteria, because of a comparable long-term overall survival rate.