Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms affecting the gastrointestinal tract. Esophageal GISTs are very rare, but recognition of esophageal GISTs has been increasing recently. We report a patient with an esophageal GIST that showed increased uptake on 18F-fluorodeoxyglucose (FDG)-positron emission tomography (PET). In this case, preoperative diagnosis was assumed to be esophageal cancer, but postoperative histopathological and immunohistochemical examination showed it to be a malignant GIST. We also found an activating mutation of kit in this patient; the mutation type was an in-frame deletion of a portion of the juxtamembrane domain (exon11). FDG-PET is useful not only for evaluating the bioactivity but also the malignant potential of esophageal GISTs.