Children in rural areas are disproportionately affected by pediatric obesity. Poor access to healthcare providers, lack of nutrition education, lower socioeconomic status, and fewer opportunities to be physically active are all unique barriers that contribute to this growing health concern. There are very few pediatric obesity interventions that have been developed that target this unique population. iAmHealthy is a family-based behavioral, nutrition and physical activity intervention developed with input from rural children and families that capitalizes on the innovative use of mobile health applications (mHealth). iAmHealthy is a 25-contact hour multicomponent intervention delivered over an 8-month period targeting 2nd-4th grade school children and their families. This paper describes the rationale, design, participant/school enrollment, and planned implementation of a randomized controlled trial of the iAmHealthy intervention in comparison to a monthly newsletter delivered through rural elementary schools. Child Body Mass Index z-score (BMIz) is the primary outcome, along with child 24-hour dietary recall, and child accelerometer-determined physical activity and sedentary behavior as secondary outcomes. The study will include 18 schools (with 8 children each) resulting in a final planned sample size of 144 children. This project also has a strong focus on dissemination and implementation science, and thus includes many measures related to the RE-AIM framework (Reach, Effectiveness, Adoption, Implementation, and Maintenance). Data collection is completed at baseline, end of intervention (8 months), and follow-up (20 months). This study is the first randomized controlled trial to deliver a rurally tailored, empirically supported, family-based behavioral intervention for pediatric obesity solely over mHealth. Registered with ClinicalTrials.gov NCT ID 03304249.