Congenital vaginal atresia is a rare congenital abnormality of the female reproductive tract due to a failure of canalisation in the urogenital sinus. We report the uncommon case of a 14-year-old girl with a primary amenorrhea associated to a cyclical pelvic pain, in whom examination objectified a vaginal cup that replaced the introitus. Ultrasound examination and magnetic resonance imaging (MRI) revealed atresia of the lower third of the vagina. The diagnosis of partial vaginal aplasia on functional uterus was retained, the patient had a perineal vaginoplasty. The evolution was satisfactory with regular cycles and improvement of pelvic pain. The decline is three years. Congenital vaginal atresia is a rare malformation classically and clinically pictured as a primary amenorrhea with chronic cyclic pelvic pain. Diagnosis is based on clinical examination and imaging. The MRI is designed to assess the importance of atresia and guide surgical management while the surgical technique aims to restore the integrity of the utero-vaginal tract and to increase the possibility of pregnancy for these patients.