Adenoid cystic carcinoma (ACC) is a relatively uncommon malignancy that most frequently arises in the salivary glands. In the genital tract, approximately 60 cases of ACC that originated from Bartholin glands have been reported to date. In this report, we describe a case of ACC that arose from Skene glands, a very rare origin for this disease. In this patient, the disease had an indolent clinical course, with few symptoms other than localized pain. During the surgical operation, the tumor was found to have invaded more extensively than had been estimated preoperatively, and it required pelvic exenteration with radical vulvectomy. Although the precise preoperative assessment and the preparation for an extended operation are difficult, they are necessary for the successful treatment of this rare disease.