Genital outflow tract obstruction is a rare cause of primary amenorrhoea. Cervical agenesis is a very rare condition often associated with atresia of vagina. Clinical diagnosis is usually difficult before surgery. Transverse vaginal septum or vaginal agenesis is also a rare condition that results from incomplete fusion between vaginal components of the mullerian ducts and urogenital sinus. If the septum is complete, the menstrual flow will be obstructed causing primary amenorrhoea. The septum is basically a membrane of fibrous connective tissue with both muscular and vascular components formed anywhere along the vagina during embryological development. Here we present a case of 18 year old female who presented with primary amenorrhea, cyclical lower abdominal pain and menouria since 5 years. There was no history of attainment of menarche. The clinical examination revealed a small, blind ending lower vagina with a tough transverse membrane separating the lower portion from the upper genital tract. The ultrasound examination revealed a normal size uterus with hematometra. The magnetic resonance imaging of pelvis confirmed the presence of hematometra and transverse vaginal septum. Transverse vaginal septum resection followed by abdomino-perineal cervicoplasty was done in this patient.