Low-grade endometrial stromal sarcoma (LGESS) accounts for only 0.2% of gynecological malignancies. Primary low-grade extrauterine endometrial stromal sarcoma (LGEESS) is rare, and its morphology varies according to the tumor's location, posing a significant diagnostic challenge for clinical pathologists. A 46-year-old female patient with bilateral ovarian cysts and multiple uterine fibroids underwent ovarian cystectomy and uterine myomectomy in 2013. Color Doppler ultrasound showed multiple uterine fibroids and bilateral ovarian cysts (left: 74 × 74 × 64 mm, right: 26 × 22 mm). Laboratory tests indicated an elevated squamous cell carcinoma associated antigen. The patient subsequently underwent a total hysterectomy and bilateral salpingo-oophorectomy. Intraoperative pathological results were diagnosed as benign ovarian cysts. Combined with the morphological, immunohistochemical, and molecular results from the paraffin section, LGEESS was determined to be the final diagnosis. We prepared a comprehensive case report on the clinicopathological features of LGEESS to provide clinical pathologists with references that can help avoid misdiagnosis or missed diagnoses.