Gastrointestinal stromal tumors (GISTs), the most common mesenchymal neoplasms of the tubular gastrointestinal tract, usually originate in the wall of the stomach or small intestine. Most GISTs harbor oncogenic mutations in either the KIT or platelet-derived growth factor receptor α (PDGFRA) tyrosine kinase receptor genes and show differentiation along the lines of the interstitial cells of Cajal. Rarely, GISTs arise primarily in the omentum, mesentery, or retroperitoneum, at which sites they are referred to as “extragastrointestinal stromal tumors” (EGISTs). However, primary intrathoracic GIST arising in the pleura or lung has not been previously reported. We describe herein, a 62-year-old male who presented with a pleural-based mass unrelated to the esophagus that was morphologically typical of a spindle-cell GIST, showing strong immunoreactivity for KIT and DOG1, and harboring an exon 11 mutation in KIT. Ten years after resection, the tumor recurred as multiple masses in the pleura and mediastinum and was marginally reexcised. The patient was then treated with adjuvant imatinib mesylate with no evidence of further recurrences 13 months later. This seems to be the first EGIST arising above the diaphragm. This case shows a potential diagnostic pitfall with therapeutic consequences.