Mullerian anomalies arise from the failure in the development of Mullerian ducts and their associated structures during organogenesis which confers adverse impact in fertility and reproductive health. Presented is a rare case of a 15 year old nulligravid, who presented with a chief complaint of severe cyclic hypogastric pain associated with primary amenorrhea. Complete clinical history, physical examination and sonographic findings pointed to a diagnosis of cervical hypoplasia associated with functioning uterine corpus and an absent vagina. Patient underwent total abdominal hysterectomy with left salpingectomy and bilateral oophorocystectomy, for hematometra, bilateral endometriotic cysts, and hematosalpinx. This case report discusses the management of cervicovaginal agenesis through a multidisciplinary approach by a team composed of an obstetrician-gynecologist, reproductive endocrinologist, pediatrician, and pediatric surgeon for proper evaluation, diagnosis, and management of this case.