Introduction: In Local Health Unit 7, human papilloma virus (HPV) vaccination campaigns for 12-year-olds have long been implemented by the vaccination services of the Department of Prevention. Due to the pressure of the COVID-19 pandemic on these services, an emergency vaccination campaign was directly managed by primary care pediatricians (PCPs). An initial evaluation of this experience was conducted. Materials and methods: Data on 12-year-olds assisted by PCPs belonging to the 2006 (pre-pandemic) and 2008 (pandemic) birth cohorts were extracted, along with HPV vaccination data. Health district, gender, citizenship, socioeconomic status, and PCPs were evaluated as possible influencing factors in a two-level logistic regression (second level: single PCP). Results: The HPV vaccination gap between males and females increased significantly for the 2008 birth cohort compared to the 2006 birth cohort (11 vs. 4 percentage points). As for PCPs, the vaccination uptake range was 4–71% for the 2008 birth cohort vs. 32–85% for the 2006 cohort. The proportion of variance explained at the second level was overall equal to 9.7% for the 2008 cohort vs. 3.6% for the 2006 cohort. Conclusions: The vaccination campaign carried out during the peak of the COVID-19 pandemic increased the HPV vaccination gaps among Health Districts, genders, and individual PCPs, probably due to a lack of homogeneity in professional practices and attitudes toward HPV vaccination. Catch-up interventions are required in the immediate term, while an equity-lens approach should be taken for reprogramming the vaccination campaign. Greater involvement of schools and families could ensure a more equitable approach and a better uptake.

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