BackgroundPediatric obesity is a multi-faceted public health concern that can lead to cardiovascular diseases, cancers, and early mortality. Small changes in diet, physical activity, or BMI can significantly reduce the possibility of developing cardiometabolic risk factors. Family-based behavioral interventions are an underutilized, evidence-based approach that have been found to significantly prevent excess weight gain and obesity in children and adolescents. Poor program availability, low participation rates, and non-adherence are noted barriers to positive outcomes. Effective interventions for pediatric obesity in primary care are hampered by low family functioning, motivation, and adherence to recommendations.MethodsThis (type II) hybrid effectiveness–implementation randomized trial tests the Family Check-Up 4 Health (FCU4Health) program, which was designed to target health behavior change in children by improving family management practices and parenting skills, with the goal of preventing obesity and excess weight gain. The FCU4Health is assessment driven to tailor services and increase parent motivation. A sample of 350 families with children aged 6 to 12 years who are identified as overweight or obese (BMI ≥ 85th percentile for age and gender) will be enrolled at three primary care clinics [two Federally Qualified Healthcare Centers (FQHCs) and a children’s hospital]. All clinics serve predominantly Medicaid patients and a large ethnic minority population, including Latinos, African Americans, and American Indians who face disparities in obesity, cardiometabolic risk, and access to care. The FCU4Health will be coordinated with usual care, using two different delivery strategies: an embedded approach for the two FQHCs and a referral model for the hospital-based clinic. To assess program effectiveness (BMI, body composition, child health behaviors, parenting, and utilization of support services) and implementation outcomes (such outcomes as acceptability, adoption, feasibility, appropriateness, fidelity, and cost), we use a multi-method and multi-informant assessment strategy including electronic health record data, behavioral observation, questionnaires, interviews, and cost capture methods.DiscussionThis study has the potential to prevent excess weight gain, obesity, and health disparities in children by establishing the effectiveness of the FCU4Health and collecting information critical for healthcare decision makers to support sustainable implementation of family-based programs in primary care.Trial registrationNCT03013309 ClinicalTrials.govElectronic supplementary materialThe online version of this article (10.1186/s13012-017-0697-2) contains supplementary material, which is available to authorized users.