School-based health centers (SBHCs) have been suggested as potential medical homes, but may experience challenges implementing the patient-centered medical home (PCMH) model. It is currently unknown if there are PCMH variations among different types of SBHCs. The purpose of this study was to examine the associations between SBHC characteristics and PCMH capacity. Using 2013–2014 National Census of School-Based Health Centers data, SBHC PCMH Index scores were calculated and used as outcomes in linear regression models examining associations between PCMH capacity and SBHC characteristics. The mean PCMH capacity score for all SBHCs was 68.59%, with higher scores in the Comprehensive Care domain than in the Care Quality domain. Managed care arrangements, Medicaid PCMH initiatives, more funding sources, and higher patient billing activity were all positively associated with overall PCMH capacity. Having higher percentages of students who are members of racial/ethnic minority groups was negatively associated with overall PCMH capacity.