Intravascular papillary endothelial hyperplasia (IPEH) is a rare benign lesion that occurs in the soft tissue of any site, including the central nervous system, extremities, head, and female reproductive system. But no case occurred in vagina was reported previously. Here, we report a case of vaginal IPEH in a 54-year-old woman who has a history of radical hysterectomy for endometrial cancer with postoperative radiotherapy. She was positive for high-risk human papillomavirus (HR-HPV) with cytology result as low-grade squamous intraepithelial lesion (LSIL), and pathology from colposcopy-directed biopsy (CDB) presented suspicious high-grade squamous intraepithelial lesion (HSIL). The colposcopy showed an 8mm neoplasm at the right apical angle of vagina. The diagnosis of IPEH was confirmed by biopsy pathology and immunohistochemistry. As the lesion was benign and rather small, we discharged the patient with annual follow-up. The case illuminated that attention should be paid to "HSIL" patients after radiotherapy to exclude the incidence of benign IPEH.