Purpose Rural Health Clinics (RHCs) and Federally Qualified Health Centers (FQHCs) provide primary care in rural areas with a shortage of providers. This paper examines whether racial and ethnic minority composition was related to changes in the supply of RHCs and FQHCs in rural counties from 2000 to 2011. Methods We conducted a retrospective cohort study of rural counties using the Area Health Resource File 2012‐2013. We examined rural counties defined as non‐Core‐Based Statistical Areas, with complete data on county characteristics for the study period (N = 1,349). Logistic regression analyses estimated associations between percentage of minority residents, and net gains and losses of RHCs and FQHCs, adjusting for total population, percentage of elderly residents, infant mortality rate, poverty rate, and physician, hospital, and clinic supply. Model estimates were used to calculate the predicted probability of outcomes across a range of minority percentage, from the 10th (≤1.6%) to 90th (≥46%) percentile of rural counties. Findings In high‐minority counties, the predicted probability of a net gain in any type of clinic was 28.6% (95% CI: 21.3‐35.8), versus 46.4% (95% CI: 40.0‐52.8) for low‐minority counties. High‐minority counties were also more likely to experience a net decline in RHCs. Conclusions During a period of substantial growth in both programs, the percentage of minority residents was negatively associated with gaining new clinics of either type. Policy makers may need to consider targeting rural minority communities for additional primary care workforce support.