Anomalies of the urogenital sinus, which is a transient feature of the early human embryological development, are rare birth defects. Urogenital sinus abnormalities commonly present as pelvic masses, hydrometrocolpos, or ambiguous genitalia and most commonly occur within the context of congenital adrenal hyperplasia. Anomalies of the urogenital sinus requires surgical repair. We experienced a case of a female newborn with congenital urogenital sinus abnormality in which the early diagnosis helped us to prevent complications by decompressing the vagina soon after birth. Antibiotic prophylaxis was sufficient to avoid infections and to decompress the genitourinary system, thus allowing a deferred elective surgery to correct the sinus.