Transverse vaginal septa are relatively rare anomalies. It has been shown to occur at different depths within the vagina. It results from vertical fusion or canalization disorder between the vaginal components of Müllerian ducts and urogenital sinus during embryological development of the vagina and can present with or without obstruction. The condition was initially described by Delaunay in 1877. The authors describe a rare case of a middle-aged female with Down's syndrome, presented with secondary amenorrhea for 3 years. Initial examination and imaging investigation revealed the presence of a transverse vaginal septum. The diagnosis was facilitated using a combination of abdominal and transvaginal ultrasound scanning and CT. And it has been revealed that she has a high rising microperforate transverse vaginal septum. Surgery and follow up was also done.