Genital warts caused by the human papillomavirus (HPV) are the most common sexually transmitted disease and have a negative impact on quality of life. Of the more than 200 different types of HPV, low‐risk types 6 and 11 are mainly responsible for the development of condyloma acuminata. Despite a large arsenal of local therapies such as numerous topical agents, CO2 laser ablation, and surgical removal, genital warts tend to be recalcitrant. HPV vaccination is mainly used as a preventive strategy to prevent genital warts, cervical cancer, and other anogenital cancers. However, in a few cases, HPV vaccination has been shown to be a good treatment alternative for patients with recalcitrant skin warts. Here we report five cases of recalcitrant genital warts that responded well to treatment with the nonavalent HPV vaccine. HPV vaccines could be beneficial as a noninvasive treatment alternative for recalcitrant genital warts.