Aims: Three licensed human papillomavirus (HPV) vaccines (Cervarix, Gardasil, and Gardasil 9) have been effectively used to prevent infection with oncogenic HPV types, however, many adverse events (AEs) have also been reported following HPV vaccination. In order to evaluate the safety of the three licensed HPV vaccines, we investigated their AE profiles based on the data from Vaccine Adverse Event Reporting System (VAERS). Methods: The AE data for Cervarix, Gardasil, and Gardasil 9 was retrieved from VAERS database respectively. The combinatorial biomedical statistical methods were used to identify the statistically significant AEs. The Gamma-Poisson Shrinker (GPS) with gender/age stratification models were developed to ascertain the serious adverse events (SAEs). The AE profiles were classified and represented by the Ontology of Adverse Events (OAE) for further analysis. Results: As of July 31, 2020, VAERS recorded 3,112, 31,606, and 6,872 AE case reports for Cervarix, Gardasil, and Gardasil 9, respectively. Our Frequentist statistical methods identified 135 Cervarix-enriched AEs, 55 Gardasil-enriched AEs, and 17 Gardasil 9-enriched AEs. Based on the OAE hierarchical classification, these AEs were clustered in the AEs that related to behavioral and neurological conditions, immune system, nervous system, and reproductive system. Combined with GPS modeling, 46 statistically significant SAEs were founded to be associated with at least one of the three vaccines. Conclusion: The results in this study cannot be used to ascertain the cause and effect relationships between the HPV vaccination and specific AEs. The hypotheses on the relationships deserver further epidemiological investigations as well as clinical trial studies.