Although gastrointestinal stromal tumor (GIST) can present with various histological characteristics, GIST mimicking perineurioma has not been previously reported. We present the case of a 47-year-old woman diagnosed with GIST after laparoscopic resection of a stomach tumor near the lesser curvature of the gastric body close to the cardia. Morphological features resembled a perineurioma. c.1504_1509 (p.A502_Y503) duplication was found in exon 9 of kinase insert domain receptor (c-KIT). This specific mutation is associated with constitutive activation of the c-KIT, which is crucial in the pathogenesis of GIST. Such unique histological characteristics broaden our understanding of the morphological diversity within GISTs and underscore the importance of considering an extended differential diagnosis when encountering atypical gastrointestinal tumors. This rare presentation may challenge conventional diagnostic criteria and could influence therapeutic strategies, emphasizing the need for comprehensive histological and molecular assessments in patient management.