Obstructive congenital anomalies of the female reproductive tract are rare and usually noticed during adolescent period for failure to see menses with cyclic abdominal pain, abdominal mass and local compressive symptoms. It is very rare for such cases to be symptomatic during early childhood from mucous collection. Congenital hydrometrocolpos (an accumulation of watery fluid in the uterus and vagina) that occurs during fetal period is a very rare condition, only with some case reports. The diagnosis is challenging and usually made late which delays the management resulting poor outcome from local compressive symptoms. We present a case diagnosed with huge congenital hydrometrocolpos secondary to low transverse vaginal septum using ultrasound by experienced radiologist and meticulous genital examination in a 5 day old neonate who had abdominal distention and difficult to pass urine since birth where incision of the septum transvaginally and drainage of the fluid was done to relieve symptoms with successful outcome.