Endometriosis may become malignant, and its diagnosis is challenging, especially in rare extra-ovarian sites like the rectum. Here, we describe the case of a 42-year-old woman who presented with intermittent left lower abdominal discomfort for six months. A colonoscopy revealed a 1.5 × 2 cm rectal lesion of high-grade intraepithelial neoplasia based on endoscopic biopsy. During surgical exploration, the mass was noted to be adherent to the posterior uterine wall, prompting partial rectal resection, total hysterectomy, and bilateral salpingectomy. Histopathological evaluation revealed a poorly differentiated adenocarcinoma infiltrating the rectum and posterior uterine myometrium, with benign endometriotic foci contiguous to the malignant component. Immunohistochemical staining supported a diagnosis of endometriosis-associated adenocarcinoma involving the rectum. Given its rarity and clinical mimicry of primary colorectal cancer, rectal endometriosis-associated adenocarcinoma presents a significant diagnostic challenge. This case underscores the importance of comprehensive surgical evaluation and detailed histopathological and immunohistochemical analyses to distinguish such tumors from primary colorectal malignancies and to guide optimal therapeutic strategies.