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Herlyn–Werner–Wunderlich (HWW) syndrome is characterized by obstructed hemivagina and ipsilateral renal anomaly, a rare congenital anomaly of the genitourinary tract, resulting from malformations of the renal tract associated with Müllerian duct anomalies. The initial symptoms of HWW frequently present after menarche and may be nonspecific, leading to a delayed diagnosis. We presented a 19-year-old female with 3-year hematuria and abdominal pain. The final diagnosis of HWW syndrome with a rare vesicovaginal fistula was made. The treatment of HWW syndrome typically involves surgical intervention. The primary treatment is resection or removal of the obstructed vaginal septum. The patient underwent excision of vaginal septum and vaginal reconstruction via hysteroscopy, as well as repair of the vesicovaginal fistula. The patient improved well after surgery and fully recovered without sequelae after 3 months. In addition, unilateral renal agenesis is one of congenital abnormalities of the kidney and urinary tract, which are the most frequent cause of chronic kidney disease (CKD) in children. This report describes a patient of HWW syndrome with rarely combined vesicovaginal fistula, and highlights the importance of early recognition and management to prevent associated complications.