Transverse vaginal septum is a rare female genital tract anomaly which may occur exclusive of any concomitant anomalies. We report the case of a pre menercheal girl who presented at our resource constrained center with primary amenorrhoea and cyclic abdominal pain. We performed a resection of the transverse vaginal septum and followed it up with the introduction of a Foley catheter in the vagina. After 4 weeks of discharge, no septal closure was present, and the menstrual flow was normal.