Background: Mayer–Rokitansky–Küster–Hauser (MRKH) syndrome typically involves Müllerian duct agenesis, whereas its coexistence with fusion anomalies such as uterus didelphys, vaginal agenesis, and cervical atresia is exceptionally rare. This case highlights the diagnostic challenge created by discordance between preoperative ultrasonography and intraoperative findings in a complex Müllerian anomaly. Case: A 26-year-old woman presented with acute-on-chronic lower abdominal pain and primary amenorrhea. Examination showed a normal vulva and a blind vaginal pouch without a visible cervix or external cervical os. Ultrasonography suggested a complex left adnexal cyst and a hypoplastic uterus, whereas magnetic resonance imaging showed a 5-cm left dermoid cyst and a retroverted uterus. Cyclic molimina suggested functional but obstructed endometrium. Intraoperative exploration revealed uterus didelphys with vaginal agenesis and total cervical atresia. A left salpingo-oophorectomy was performed for the dermoid cyst. Discussion: The case demonstrates the limitations of ultrasonography for detailed mapping of complex Müllerian duct anomalies, particularly when adnexal masses obscure pelvic anatomy. The combination of a blind vaginal pouch and cyclic pain indicates complete outflow tract obstruction and creates major reproductive and reconstructive challenges. Conclusion: Careful physical examination, advanced imaging, and intraoperative confirmation are essential when imaging findings are discordant with clinical symptoms. Precise anatomical mapping is critical for fertility counseling and planning future reconstructive treatment.