Although several authors have reported on neovaginal prolapse, the reasons for such prolapse are not understood. We report a rare case of sigmoid neovagina 40 years after operation. A 22-year-old woman with vaginal agenesis underwent vaginoplasty using sigmoid colon. Almost 40 years after initial operation, she came to our hospital complaining of a bearing-down sensation and an increase in vaginal discharge. At vaginal examination, the neovagina protruded approximately 5 cm beyond the hymen, but the apex of the neovagina was not prolapsed. A resection of the redundant neovagina was performed. By histopathologic examination of the excised specimen, we recognized thick colonic mucosa. We diagnosed the prolapsed vagina as hyperplasia of colonic mucosa. Hyperplasia of transplanted colonic epithelium can be a cause of neovaginal prolapse even 40 years after operation.