Colonic mesenchymal tumors represent a diagnostic challenge due to their rarity and the overlap of clinical and imaging features with other subepithelial lesions, particularly gastrointestinal stromal tumors (GISTs). Histopathological evaluation remains essential to guide appropriate management and establish prognosis. We report the case of a 64-year-old woman with a three-year history of abdominal distension, altered bowel habits, and occult gastrointestinal bleeding. Repeated colonoscopies revealed a large subepithelial lesion in the transverse colon, highly suggestive of GIST, though repeated biopsies were nondiagnostic. As symptoms persisted and intestinal obstruction developed, the patient underwent a laparoscopic left hemicolectomy with intracorporeal anastomosis. Final histopathological analysis revealed a benign colonic lipoma. The patient's postoperative course was uneventful, with marked improvement in quality of life. This case illustrates the clinical difficulty of distinguishing between GISTs and colonic lipomas, as endoscopic imaging and biopsy often fail to yield a definitive diagnosis. Tumor size, endoscopic features, and obstructive symptoms guided the therapeutic decision. Surgical resection resolved the obstruction and provided a definitive diagnosis, offering both clinical and psychological benefits. This case highlights the importance of considering colonic lipoma in the differential diagnosis of large subepithelial colonic lesions and reinforces the role of surgery in both treatment and diagnostic certainty.