Müllerian duct anomalies (MDAs) are congenital disorders of the female genital tract resulting from abnormal embryological development of the Müllerian ducts. These abnormalities occur in approximately 0.5%–5.0% of the general population. The case involves a 16-year-old Middle Eastern female referred to the clinic due to primary amenorrhea and lower abdominal pain. Upon evaluation, we identified a congenital anomaly known as uterine didelphys with a transverse vaginal septum. Uterine didelphys is a type of Müllerian duct anomaly characterized by the complete duplication of the uterus, cervix, and sometimes the vagina. Our case is exceptional, as most reported instances feature a longitudinal vaginal septum with uterine didelphys, and it is rare to find both longitudinal and transverse vaginal septa. The combination of uterine didelphys with only a transverse vaginal septum is extremely rare. To the best of our knowledge, this is only the third reported case of its kind.