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Abstract Background A greater understanding of the county-level differences in human papillomavirus (HPV) vaccination rates could aid targeting of interventions to reduce HPV-related cancer disparities. Methods We conducted a mixed-methods study to compare the stakeholder-reported barriers and efforts to increase HPV vaccination rates between counties within the highest, middle, and lowest HPV vaccine initiation (receipt of the first dose) rates among 22 northern Florida counties. Between August 2018 and April 2019, we recruited stakeholders (n = 68) through purposeful and snowball sampling to identify potential participants who were most knowledgeable about the HPV vaccination activities within their county and would represent a variety of viewpoints to create a diverse picture of each county, and completed semi-structured interviews. County-level HPV vaccine initiation rates for 2018 were estimated from the Florida Department of Health’s immunization registry and population counts. Implementation strategies were categorized by level of importance and feasibility using the Expert Recommendations for Implementing Change (ERIC) taxonomy. We compared the barriers and implementation strategies for HPV vaccination between tercile groups of counties by HPV vaccine initiation rates: highest (18 stakeholders), middle (27 stakeholders), and lowest (23 stakeholders). Results The majority of the 68 stakeholders were female (89.7%), non-Hispanic white (73.5%), and represented a variety of clinical and non-clinical occupations. The mentioned barriers represented five themes: healthcare access, clinician practices, community partnerships, targeted populations, and cultural barriers. Within themes, differences emerged between county terciles. Within healthcare access, the highest rate county stakeholders focused on transportation, lowest rate county stakeholders focused on lack of clinicians, and middle county stakeholders mentioned both. The number of ERIC quadrant I strategies, higher feasibility, and importance described decreased with the tercile for HPV vaccination: highest = 6, middle = 5, and lowest =3 strategies. Conclusions The differing barriers and strategies between the highest, middle, and lowest vaccination rate counties suggest that a tailored and targeted effort within the lowest and middle counties to adopt strategies of the highest rate counties may reduce disparities.