INTRODUCTION: The co-occurrence of a unicornuate uterus with a noncommunicating, functioning rudimentary horn and VACTERL association represents an extremely rare condition, with only 3 similar cases reported in the literature. CASE: The patient, aged 12 years and 9 months, presented with pelvic pain and severe dysmenorrhea, which started shortly after her menarche at 12 years and 4 months. At birth, she exhibited 3 characteristic components of VACTERL association: bronchoesophageal fistula/esophageal atresia, anal atresia, and polydactyly. Magnetic resonance imaging revealed a unicornuate uterus with a noncommunicating, functioning rudimentary horn, and subsequently, VACTERL association was diagnosed. The rudimentary horn was laparoscopically excised 8 months post-menarche, resulting in symptom resolution. CONCLUSION: Health care providers should consider the possibility of genital anomalies when diagnosing VACTERL association, especially in cases presenting with severe early dysmenorrhea.