BACKGROUND Endometriosis is a common cause of chronic pelvic pain among women globally. Pharmacological therapy for endometriosis includes non-steroidal anti-inflammatory drugs (NSAIDs) and hormonal contraceptives, while surgical therapy often involves either laparoscopic excision and ablation of endometriosis implants or open surgery. Surgical therapy is one of the mainstays of treatment especially for extrapelvic endometriomas. However, little guidance exists for the treatment of non-palpable or intermittently palpable lesions of this nature. CASE REPORT A 33-year-old woman with a previous cesarean section presented with complaints of intermittent discomfort in the area between her umbilicus and the surgical incision, for the previous 7 years, that worsened during her menstrual cycle. A 3×3-cm area of fullness was only intermittently palpable during various clinic visits, but was visualizable on computed tomography and magnetic resonance imaging. Given the lesion's varying palpability, a Savi Scout radar localization device was placed into the lesion pre-operatively to aid with surgical resection. The mass was excised, pathologic examination revealed endometrial tissue, and the patient had an uncomplicated postoperative course with resolution of her symptoms. CONCLUSIONS Surgical removal of extrapelvic endometrioma lesions can be made difficult by varying levels of palpability or localizability due to a patient's menstrual cycle. The Savi Scout, most commonly used in breast mass localization, is a useful tool in guiding surgical excision of non-palpable or intermittently palpable extrapelvic endometrioma lesions.