Here, we present a case of a 40-year-old female patient who presented with complaints of bleeding per rectum, pain during defecation, and something coming out per rectum for the past 3 months. On per rectal examination, a polypoidal growth was seen coming out of the rectum. The clinical diagnosis was given as a rectal polyp. The patient underwent surgical resection of rectal polyp postclinical diagnosis. The excised specimen was received in the Histopathology Department of Sumandeep Vidyapeeth. Here, we performed the gross and microscopic examination of the polyp. The histopathological diagnosis of malignant gastrointestinal stromal tumor (GIST) was given after confirmation with immunohistochemistry. GISTs are rare mesenchymal tumors commonly found in the stomach and small intestine, with rectal involvement being exceedingly uncommon. This report aims to highlight the diagnostic challenges, treatment strategies, and outcomes associated with this unusual presentation.