An 18-year-old female presented with primary amenorrhea and progressive cyclic abdominal pain, which prompted emergency exploratory laparotomy. Intraoperative findings revealed absent cervix and vagina, partial bicornuate uterus, hematometra, left tubal endometriosis, ruptured left endometrioma and left renal agenesis. Left salpingectomy, left oophorocystectomy, hysterotomy, evacuation of menstrual blood and transverse loop colostomy were performed. Depo-medroxyprogesterone acetate was administered to suppress menses. On re-exploration, utero-rectovestibular fistula anastomosis was described with the distal rectovestibular fistula functioning as a neovagina. Cyclic menses occurred thereafter. Endorectal pull-through with anoplasty was performed after the fistulous tract healed. To the best of our knowledge, this is the first reported case of cervico-vaginal agenesis associated with imperforate anus and rectovestibular fistula. Early diagnosis and surgery are necessary to avoid complications such as endometriosis. The aim was to preserve fertility with conservative management.