School-Based Health Centers (SBHCs) are important healthcare providers for children in medically underserved communities. While most existing research on SBHCs has focused on urban environments, this study protocol proposes a mixed-methods, multi-level research framework to evaluate the role of SBHCs in addressing health disparities among underserved children and adolescents in rural communities. The study area includes four high-poverty rural counties in New York State served by Bassett Healthcare Network that permits a comparison of school districts with SBHCs to those without SBHCs, all served by providers within the Bassett Healthcare Network. We employ a human ecological framework that integrates the micro layer of individuals and families, the meso layer of school districts and community institutions, and the macro layer of local and state policies. Our research framework first identifies the socioecological health risk factors, and then proposes innovative strategies to investigate how SBHCs impact them. We propose evaluating the impact of SBHCs on the individual (micro) level of child healthcare utilization using patient records data. At the meso level, we propose to investigate how School-SBHCs partnership may facilitate greater cross-agency collaboration and broader structural and social determinist of health to address health disparities. At the macro level, we propose to assess the impact of SBHCs and cross-agency collaboration on outcomes associated with a culture of community health. This study protocol will enable researchers to assess how SBHCs reduce rural health disparities, and provide evidence for organizational and public policy change.