BACKGROUND: Cardiovascular disease is the leading cause of death in the United States and places substantial burden on the health care system. Rural populations, especially women, have considerably higher rates of cardiovascular disease, influenced by poverty, environmental factors, access to health care, and social and cultural attitudes and norms. METHODS/DESIGN: This community-based study will be a two-arm randomized controlled efficacy trial comparing a multi-level, community program (Strong Hearts, Healthy Communities) with a minimal intervention control program (Strong Hearts, Healthy Women). Strong Hearts, Healthy Communities was developed by integrating content from three evidence-based programs and was informed by extensive formative research (e.g. community assessments, focus groups, and key informant interviews). Classes will meet twice weekly for one hour for 24 weeks and focus on individual-level skill building and behavior change; social and civic engagement are also core programmatic elements. Strong Hearts, Healthy Women will meet monthly for hour-long sessions over the 24 weeks covering similar content in a general, condensed format. Overweight, sedentary women 40 years of age and older from rural, medically underserved communities (12 in Montana and 4 in New York) will be recruited; sites, pair-matched based on rurality, will be randomized to full or minimal intervention. Data will be collected at baseline, midpoint, intervention completion, and six-month, one-year, and eighteen months post-intervention. The primary outcome is change in body weight; secondary outcomes include physiologic, anthropometric, behavioral, and psychosocial variables. In the full intervention, engagement of participants' friends and family members in partnered activities and community events is an intervention target, hypothesizing that there will be a reciprocal influence of physical activity and diet behavior between participants and their social network. Family members and/or friends will be invited to complete baseline and follow-up questionnaires about their health behaviors and environment, height and weight, and attitudes and beliefs. DISCUSSION: Strong Hearts, Healthy Communities aims to reduce cardiovascular disease morbidity and mortality, improve quality of life, and reduce cardiovascular disease-related health care burden in underserved rural communities. If successful, the long-term goal is for the program to be nationally disseminated, providing a feasible model to reduce cardiovascular disease in rural settings. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02499731 Registered on July 1, 2015.