This study evaluated the long-term effectiveness of the three-dose 4vHPV vaccine eleven years after a 2012 pilot program in Mongolia. It assessed women aged 24–28 for protection against HPV16/18 using self-collected vaginal samples and GenExpert testing. Results showed 88% effectiveness against vaccine-type HPV but no cross-protection against other high-risk types. Knowledge of HPV and cervical cancer remained low, despite high acceptance of self-sampling methods. Findings highlight the need for awareness efforts ahead of Mongolia’s planned HPV vaccine reintroduction in 2024.