Human papillomavirus (HPV) can be detected in most of cervical cancers. Due to antiviral, antimutagenic, and proapoptotic activities of myrtle, this study was designed to investigate the effect of a herbal suppository based on myrtle in cervicovaginal HPV infections. This study was performed as a double‐blind randomized trial at the Clinic of Traditional Medicine in Mashhad University of Medical Sciences between 2016 and 2017. Sixty women, 18 to 50 years old, with cervicovaginal HPV infection, were included and randomly allocated to two groups. Sixty placebo or herbal vaginal suppositories were prescribed for 3 months (20 suppositories at each menstrual cycle). Each herbal vaginal suppository contained 10% of myrtle aqueous extract and 0.5% of myrtle essential oil. The HPV test and colposcopic findings were evaluated after treatment. There was no difference between two groups as regards lesion site, diagnosis time of disease, and HPV type before intervention (p ≥ 0.05). At the end of the study, the HPV test was negative in 92.6% and 62.6% of the intervention and placebo groups, respectively (p = 0.036). The change in cervical lesion size was 71.4% and 30.4% in the intervention and placebo groups, respectively, based on colposcopic findings (p = 0.015). It seems that herbal suppository can speed up virus clearance and can be effective in treating HPV infection.