Background: The Healthy, Hunger-Free Kids Act of 2010 (HHKA) required schools to make changes to meals provided to children. Rural school districts have limited resources, with increased obesity rates and local food insecurity. In this study we sought to understand the perceptions of rural food service directors and the barriers to implementing the changes. Methods: Food service directors from rural school districts were invited to complete a semistructured telephone interview and online survey. A total of 51 respondents completed both, 6 completed only the online survey, and 16 completed only the telephone interview. Qualitative interview data were analyzed through open thematic coding; descriptive statistics were calculated for the quantitative data. Results: Food service directors mostly perceived the changes as negative, challenging, and burdensome. They believed that the changes resulted from concern about childhood obesity, which they did not view as a problem for their students. Diverse challenges were reported related to cost, preparation, and student preference. Conclusions: Food service directors in isolated, rural areas need support to enhance understanding of HHKA requirements, build professional networks to learn from one another, and communicate with students, families, and other stakeholders. Future efforts should focus on changing perceptions and supporting directors in order to make implementation a success.