(1) Background: Premature ovarian insufficiency (POI) has been linked to human papilloma virus (HPV) vaccination in small case-reports. The aim of this meta-analysis was to evaluate the risk of POI after HPV vaccination. (2) Methods: Electronic searches in MEDLINE Scopus, LILACS, ClinicalTrials.gov, EMBASE, PROSPERO, Cochrane CENTRAL and other registries were searched from inception to September 2022. Inclusion criteria were cohort studies of female children or adolescents vaccinated with quadrivalent (4vHPV), bivalent (2vHPV) or 9-valent (9vHPV) vaccine and compared to unvaccinated, other HPV vaccine, or vaccinated with other childhood vaccine girls. Primary outcome was risk of POI after vaccination. (3) Results: Four studies, including 1,253,758 patients, were included. Overall, there was no significant risk for POI between 4vHPV and controls (unvaccinated or other vaccines) (RR 0.47 (95% CI 0.14 to 1.59) I = 75%), or unvaccinated only controls (RR 0.75 (95% CI 0.22 to 2.49) I = 26%). One study reported a significant reduction of POI risk for 4vHPV relative to the other childhood vaccinations (RR 0.03 (95% CI 0.00 to 0.21)); meanwhile, one study showed no increased risk with 4vHPV relative to 2vHPV and 9vHPV (RR 0.93 (95% CI 0.33 to 2.64)). (4) Conclusions: 4vHPV vaccination does not seem to increase risk of POI relative to unvaccinated people or other childhood vaccines. No difference was seen with 4vHPV vaccine relative to 2vHPV and 9vHPV. Moreover, the risk of POI after HPV vaccination is relatable to worldwide incidence, giving reassurance about safety.