The Patient-Centered Medical Home (PCMH) is a new model for primary care delivery intended to improve the care experience for both patients and providers, improve the health of populations, and reduce health care costs. Adopting the PCMH model into practice requires considerable investment of time and resources which often act as barriers for many small primary care practices; especially in rural areas. Few studies have examined performance of the PCMH model in rural clinics that have successfully implemented the model. It is important to obtain a comprehensive understanding of how context from the surrounding environment relates to implementation and performance of the model and whether there are differences between rural and urban primary care clinics. This study used a sequential explanatory mixed methods approach to assess differences in performance of the Patient Aligned Care Team (PACT) model between rural and urban primary care clinics within the Veterans Health Administration (VHA). Generalized Estimating Equations with repeated measures were used to estimate associations between rurality and five process-oriented endpoints among a national sample of 891 VHA primary care clinics. Results indicate that, after adjusting for patient characteristics and clinic structural capacity, clinics located in large rural or small/isolated rural areas demonstrated difficulty with enhancing access through use of non-traditional encounters (i.e. telephone visits, group visits, or secured messaging) and facilitating care coordination through post-discharge follow-up compared to urban clinics. Findings also suggest that rural clinics were more likely to struggle to meet system-wide performance standards for these same two PACT-related processes than their urban counterparts. A multiple-case study of five VHA primary care clinics was conducted to obtain a contextual understanding of the relationships between rurality and performance of PACT processes from the perspective of primary care staff engaged in PACT implementation. A comparison of the experiences of staff across the five cases revealed cross-cutting themes that are important to understanding the implementation and performance of PACT-related processes within these clinics. These themes included: both rural and urban clinics experience distance-related barriers; patient preferences and behavior impact performance of PACT-related processes; and primary care clinics experience frequent change. Findings from this qualitative assessment highlight the importance of understanding the unique context and circumstances experienced by each clinic and how they relate to performance and implementation of the PACT model. Insights gained through the qualitative assessment revealed that performance of PACT is influenced by complex relationships with both internal and external context. Combination of both quantitative and qualitative methods provided a more comprehensive understanding of these relationships beyond what could have been learned from a solitary assessment of standardized metrics by gaining additional context directly from the voices of those engaged in PACT care delivery. Identifying differences in PACT performance between rural and urban clinics calls attention to the possibility of unique advantages and challenges for PACTs delivering care to rural patients which need further exploration. Findings from this study contribute to the current understanding of PCMH implementation in rural settings by moving beyond the barriers related to structural capacity to performance of processes aligned with PCMH principles. More widespread implementation of PCMH will require additional attention to the complex relationships between the PCMH and surrounding context in order for primary care practices to successfully implement the model.