The introduction of human papillomavirus vaccines revolutionized cervical cancer prevention. Our research hypothesis is that HPV vaccination affects the remission of HPV in cervical swabs. We provide a prospective, ongoing, 24-month, non-randomized study in HPV-positive women. We enrolled 60 patients with positive HPV swabs from the cervix (fifty-one vaccinated with the nine-valent vaccine against HPV and nine unvaccinated). Using an enzyme-linked immunosorbent assay, we determined IgG class antibodies of HPV in the patients’ serums. Persistent HPV infection after vaccination was significantly less frequent in the nine-valent vaccinated group (23.5%) compared to the control group (88.9%; p < 0.001). Antibody level after vaccination was significantly higher in the vaccinated patients compared to the control group. The reactive antibody level was seen in the case of all patients in the vaccinated group and one-third of the unvaccinated group (33.3%, n = 3). The vaccination of HPV-positive patients may increase the chance of HPV remission in cervical swabs and may be a worthwhile element of secondary prevention in HPV-positive patients.