Most gastrointestinal stromal tumors (GISTs) arise from the proper muscle layer of the upper gastrointestinal (GI) tract and have a low malignant potential. They are sometimes accompanied by symptoms, but in most cases are detected by chance. Endoscopic surgery of subepithelial tumors in the upper GI tract has been actively performed, and its merits include the need for fewer medical devices compared with other surgical procedures and post-resection organ preservation. However, because endoscopic procedures are still limited to small or pilot studies, a multidisciplinary approach combining laparoscopy and endoscopy is needed for more effective and pathologically acceptable management of GISTs. Many new endoscopic surgeries have been developed, and this review describes the current status of and the new approaches for endoscopic surgery of GISTs in the upper GI tract.