Following the 2019 ACIP recommendation expanding HPV vaccination to adults aged 27–45 through shared decision-making (SDM), there is limited understanding of how these guidelines are implemented in rural communities. This study surveyed 142 mid-adult patients at two federally qualified health centers and 93 clinicians in New Hampshire and Vermont to assess perceptions of SDM and barriers to vaccination. Patients most frequently cited inadequate insurance coverage and perceived ineligibility as reasons for not receiving the vaccine. Clinicians reported inconsistent awareness of expanded eligibility, and SDM was more often practiced with female patients than with male patients, reflecting persistent gender-based knowledge gaps. Both patient and clinician groups viewed SDM as a facilitator for vaccination uptake. These findings highlight the need for educational tools addressing cost transparency, eligibility clarification, and gender-neutral HPV vaccine messaging. Future interventions should support clinicians in effectively conducting SDM within rural primary care settings to improve mid-adult HPV vaccination coverage.