This study explored the implementation of the human papillomavirus (HPV) vaccine school-entry requirement in Puerto Rico during the COVID-19 pandemic. We conducted 26 semi-structured interviews with stakeholders and community-based organizations from August 2021 to March 2022. The interview guide was developed using the 2009 Consolidated Framework for Implementation Research (CFIR). The interviews were recorded and transcribed in Spanish. Data were analyzed using applied thematic techniques. These themes included the following: (i) Intervention characteristics: Participants noted that the school-entry requirement was effective in increasing vaccination uptake prior to the pandemic. Issues with the immunization registry were noted; (ii) Outer setting: External influences, access barriers, and an increase in HPV vaccine exemptions since the implementation of the COVID-19 vaccine were discussed; (iii) Inner setting: Communication within organizations and HPV vaccination efforts improved as the pandemic progressed; (iv) Characteristics of individuals: Most agreed with the school-entry requirement, including exemptions; and (v) Process: Results showed the need to reinforce the population’s education about HPV and the vaccine. Implementation of the policy was challenging during the early stages of the pandemic due to measures enacted to stop the spread of COVID-19 and focus on the COVID-19 vaccine. Efforts to increase HPV vaccine should focus on increasing HPV vaccine education and creating collaborations.