Obstructed hemivagina and ipsilateral renal agenesis syndrome is a rare complex of structural abnormalities of female urogenital tract. Moreover, delayed treatment of this condition can reportedly lead to pelvic infection, endometriosis, and infertility. We present a rare case of obstructed hemivagina and ipsilateral renal agenesis syndrome wherein appropriate treatment was initiated early due to the identification of left renal agenesis. A 14-year-old girl visited the gynecology department due to worsening left lower abdominal pain after menarche. She was diagnosed with renal dysplasia in the pediatric department at the ages of 3 and 9 years, and it was recommended that she visits the gynecology department right after menarche. She experienced her first menarche at the age of 14 years. Imaging studies revealed uterine didelphys with occlusion of the left vagina and formation of hematocolpos. Additionally, hematomas were observed in the left uterine cavity and the left fallopian tube; left renal agenesis was confirmed. Based on these findings, we diagnosed this patient with obstructed hemivagina and ipsilateral renal agenesis syndrome and performed a surgical incision and excision of the closed left vaginal wall, resulting in the disappearance of the hematocolpos. Approximately 2 years postoperatively, the patient has remained recurrence-free. Early diagnosis and treatment are crucial for preserving fertility in patients with obstructed hemivagina and ipsilateral renal agenesis syndrome, and early referral to the obstetrics and gynecology department is recommended if renal dysplasia is detected during childhood.