Abstract Background Young children who are overweight are at increased risk of becoming obese and developing type 2 diabetes and cardiovascular disease later in life. Therefore, early intervention is critical. This paper describes the rationale, design, methodology, and sample characteristics of a 5-year cluster randomized controlled trial being conducted in eight elementary schools in rural North Carolina, United States. Methods/Design The first aim of the trial is to examine the effects of a two-phased intervention on weight status, adiposity, nutrition and exercise health behaviors, and self-efficacy in overweight or obese 2nd, 3 rd, and 4th grade children and their overweight or obese parents. The primary outcome in children is stabilization of BMI percentile trajectory from baseline to 18 months. The primary outcome in parents is a decrease in BMI from baseline to 18 months. Secondary outcomes for both children and parents include adiposity, nutrition and exercise health behaviors, and self-efficacy from baseline to 18 months. A secondary aim of the trial is to examine in the experimental group, the relationships between parents and children's changes in weight status, adiposity, nutrition and exercise health behaviors, and self-efficacy. An exploratory aim is to determine whether African American, Hispanic, and non-Hispanic white children and parents in the experimental group benefit differently from the intervention in weight status, adiposity, health behaviors, and self-efficacy. A total of 358 African American, non-Hispanic white, and bilingual Hispanic children with a BMI ≥ 85th percentile and 358 parents with a BMI ≥ 25 kg/m2 have been inducted over 3 1/2 years and randomized by cohort to either an experimental or a wait-listed control group. The experimental group receives a 12-week intensive intervention of nutrition and exercise education, coping skills training and exercise (Phase I), 9 months of continued monthly contact (Phase II) and then 6 months (follow-up) on their own. Safety endpoints include adverse event reporting. Intention-to-treat analysis will be applied to all data. Discussion Findings from this trial may lead to an effective intervention to assist children and parents to work together to improve nutrition and exercise patterns by making small lifestyle pattern changes. Trial registration NCT01378806.