Objective We compared the clinicopathologic features between mesenchymal tumors located in the esophagogastric junction (EGJ) and upper stomach, that had been removed surgically. Methods Thirty-five patients with a submucosal tumor (SMT) of the stomach, including the EGJ, were surgically treated over the last decade. Of these, 23 patients with SMTs located in the upper third of the stomach (n = 15; UG-group) and EGJ (n = 8; EGJ-group) were studied. Results The mean age was younger in the EGJ-group than in the UG-group, and the EGJ-group frequently showed symptoms. Histopathologically, 4 gastrointestinal stromal tumors (GISTs) and 4 leiomyomas were observed in the EGJ-group, while 14 GISTs and one schwannoma were observed in the UG-group (p = 0.0096). Two tumors macroscopically showed a horseshoe or spiral type in the EGJ-group, while all tumors showed a ball/ball-like appearance in the UG-group. Regarding surgical procedures, 7 patients underwent laparotomy in the EGJ-group, while 9 patients underwent laparoscopic surgery in the UG-group. The mean operating time was longer and operative bleeding was greater in the EGJ-group than in the UG-group, respectively (p = 0.0015 and p = 0.0095). Postoperative complications were frequently observed in the EGJ-group. The EGJ-group showed no patients with recurrence and/or metastasis after surgery, while three cases with GISTs had them in the UG-group. In GISTs, the mean mitotic index of the UG-group was relatively more than that of the EGJ-group and a case was classified into the high-risk group, although there was no significance in the risk classification between the two groups. Conclusion SMTs included GISTs and leiomyomas in the EGJ, while the majority demonstrated GISTs in the upper stomach. SMTs of the EGJ were removed by a tailored approach to prevent recurrence as well as postoperative complications. The biological behavior of GISTs may be different between the EJG and stomach.