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Introduction: In 2008, Mexico initiated its national HPV vaccination program targeting adolescent girls. This study aims to evaluate the current status of the program, analyzing trends in vaccine acquisition, administration, and coverage over a 16-year period. Materials and Methods: A retrospective longitudinal study was conducted using secondary data from 2008 to 2023. Official records from three major public health institutions—IMSS, ISSSTE, and SSA—were reviewed to assess HPV vaccine procurement and administration. Results: Significant fluctuations were identified in the number of doses acquired, administered, and the corresponding coverage rates. A marked decline was observed between 2019 and 2021, followed by a sharp increase in 2022 and 2023. Over the entire period, an estimated 6.8 million doses were not administered to the intended target population. Furthermore, 2.6 million doses were administered in excess of the number officially acquired, indicating possible discrepancies in data reporting or vaccine inventory management. Discussion: The findings revealed substantial inconsistencies in vaccine procurement, administration, and coverage across institutions. While IMSS and ISSSTE consistently reported coverage below the theoretical target, SSA occasionally exceeded expectations, potentially compensating for deficits elsewhere. Nevertheless, national coverage remained inadequate in several years, with notable disparities between institutions. These gaps highlight systemic weaknesses in program coordination, planning, and data transparency, contributing to millions of unvaccinated individuals. Conclusions: This study offers a comprehensive analysis of Mexico’s HPV vaccination program, uncovering critical irregularities in its implementation. Challenges include inaccurate target population estimation, inconsistencies between vaccine acquisition and administration, and limited data reliability. Despite some progress in recent years, particularly in the post-pandemic years, the program requires urgent restructuring. This includes implementing a national catch-up strategy, expanding vaccine eligibility, and strengthening surveillance systems to ensure equitable and effective coverage toward the elimination of cervical cancer. Full article