Gastrointestinal Stromal Tumors (GISTs) are rare neoplasms accounting for only 0.1 to 3 % of Gastrointestinal Malignancies but they account for 80% of Gastrointestinal Mesenchymal Neoplasms. The only principle and curative treatment available for GISTs is Surgical R0 Clearance.Laparoscopic Resection of GIST is routinely advocated only for tumours at favourable locations and smaller sizes(Less than 5 cm). But the Gastro-Esophageal (GE)Junctional tumours poses a special risk of involving the Lower Esophageal sphincter while resection, thereby causing Reflux or late Stenosis. These tumours had been traditionally dealt with more morbid Total Esophagectomy and Gastrectomy procedures. But with advent of newer refined techniques of Laparoscopy and its instrumentation, these tumours can be handled with minimally invasive approaches without compromising the oncological and functional perspectives. We here discuss two of such innovative approaches to deal with the GE Junctional GISTs in our experience, namely the Trans-gastrotomy stapled Resection and Endoscopy assisted Laparoscopic Wedge Resection.