Congenital anomalities of the vagina are rare congenital anomalies. Women born with this anomaly present with collection of blood in the uterine cavity or hematometra and pelvic pain. Presented is a case of a 12-year old girl with hypogastric pain and primary amenorrhea complicated by vaginal agenesis. She was managed conservatively by creating a neovagina with the use of bipudental flap or Modified Singapore flap. Management can be non-surgical or surgical but the management of congenital vaginal agenesis remains controversial. The decision to do a conservative surgical procedure or a hysterectomy depends on the clinical profile of the patient, the expertise of the surgeons, the extent of the anomaly, and it's association to other congenital anomalies.