Gastrointestinal Stromal Tumors (GISTs) pose intricate diagnostic challenges due to their diverse clinical presentations. In this case, a 52-year-old female patient presented with lower abdominal pain, dyspeptic symptoms, and significant weight loss. Initial imaging suggested gynecological malignancy, leading to a Total Abdominal Hysterectomy and Bilateral Salpingo-Oophorectomy (TAH + BSO). However, during surgery, the uterus was found to be atrophic and the ovaries normal, contrary to the initial diagnosis, and revealed an 8.6 cm GIST. The tumor was classified as AFIP Risk 3a, pT3NxMx, with low mitotic activity. This case highlights the importance of a multidisciplinary approach in managing complex clinical cases and emphasizes the need for collaboration and adaptability.