Background In medically underserved regions such as Appalachia, cervical cancer incidence and mortality are higher than the general U.S. population; therefore, it is important for pediatricians to encourage parents to have their daughters vaccinated against the human papillomavirus (HPV). Unfortunately, little is known about the predictors of pediatricians’ encouragement of the HPV vaccine among medically underserved populations. The current study compared attitudes and behaviors of pediatricians with practices in Appalachia with those in non-Appalachia to identify potential strategies for reducing health disparities. Methods A survey was conducted with 334 pediatricians located in Appalachia and non-Appalachia counties to examine how prior behavior, perceived susceptibility, severity, self-efficacy, response-efficacy, and behavioral intentions are related to self-reported vaccine encouragement. Results Pediatricians in Appalachia perceived their patients to be less susceptible to HPV and reported lower rates of HPV encouragement than pediatricians in non-Appalachia. In addition, self-efficacy had a significant indirect association with vaccine encouragement for pediatricians in non-Appalachia. Conclusion This study’s findings emphasize the importance of increasing Appalachian pediatricians’ awareness of their patients’ susceptibility to HPV. Broader efforts to increase encouragement of the HPV vaccine among pediatricians should focus on promoting self-efficacy to encourage the HPV vaccine to parents of young females.