BACKGROUND Extragastrointestinal stromal tumors (E-GISTs) are a rare subtype of gastrointestinal stromal tumors (GISTs) that develop outside of the gastrointestinal tract from interstitial cells of Cajal, exhibiting specific markers such as CD117 and DOG1. These tumors often present diagnostic challenges, particularly when their clinical manifestations mimic other abdominal conditions, such as acute appendicitis. CASE REPORT A 75-year-old male patient with a history of multiple comorbidities presented to the Emergency Department with symptoms of chronic pain in the right lower quadrant. Imaging studies, including computed tomography scans, revealed a large heterogeneous density mass measuring 11.3×9.2 cm in the right lower quadrant and a dilated appendix with wall thickening. Subsequent surgical resection with right hemicolectomy and primary anastomosis was performed, and postoperative considerations included adjuvant therapy with imatinib, due to spindle cell morphology and high mitotic activity. Histopathological examination and immunohistochemical staining confirmed the diagnosis, showing positive CD117, DOG1, Bcl-2, D2-40, and WT1 markers. CONCLUSIONS This case report aims to highlight the complexities in diagnosing E-GISTs with atypical presentations and emphasizes the critical role of comprehensive imaging and histopathological assessments in achieving an accurate diagnosis and guiding appropriate management strategies. The successful diagnosis and management highlight the critical role of imaging modalities and immunohistochemical analysis in guiding treatment decisions, while postoperative care, including targeted therapy, is crucial for reducing the risk of recurrence and improving patient outcomes. Future research should focus on optimizing postoperative management strategies and investigating the potential of intraoperative biopsies for tumors abutting adjacent structures.