Herlyn-Werner-Wunderlich syndrome is a rare congenital anomaly of the urogenital tract, which is characterized by the triad of uterus didelphys, obstructed hemivagina, and ipsilateral renal agenesis. It usually presents at puberty with pelvic pain, dysmenorrhea, and a vaginal or pelvic mass. Although rare, it may present with purulent vaginal discharge due to secondary infection of the obstructed hemivagina, making diagnosis difficult. A careful pelvic examination to identify the cervix and vagina is the key to the diagnosis of Mullerian duct anomalies and magnetic resonance imaging can provide additional useful information. The optimal treatment is full excision and marsupialization of the obstructing vaginal septum so that both uteri can drain through the patent vagina. The authors report a case of a 22-year-old female with an unusual presentation of Herlyn-Werner-Wunderlich syndrome complicated by pyocolpos, which was successfully managed by vaginal septum resection and drainage of pus.