Background: Obesity is mainly attributed to environmental factors. In developed countries, the time spent on physical activity tasks is decreasing, whereas sedentary behaviour patterns are increasing. The purpose of the intervention is to evaluate the effectiveness of an intensive family-based behavioural multicomponent intervention (Nereu programme) and compared it to counselling intervention such as a health centre intervention programme for the management of children"s obesity. Methods/Design: The study design is a randomized controlled multicenter clinical trial using two types of interventions: Nereu and Counselling. The Nereu programme is an 8-month intensive family-based multi-component behavioural intervention. This programme is based on a multidisciplinary intervention consisting of 4 components: physical activity sessions for children, family theoretical and practical sessions for parents, behaviour strategy sessions involving both, parents and children, and lastly, weekend extra activities for all. Counselling is offered to the family in the form of a monthly physical health and eating habits session. Participants will be recruited according the following criteria: 6 to 12 year-old-children, referred from their paediatricians due to overweight or obesity according the International Obesity Task Force criteria and with a sedentary profile (less than 2 hours per week of physical activity), they must live in or near the municipality of Lleida (Spain) and their healthcare paediatric unit must have previously accepted to cooperate with this study. The following variables will be evaluated: a) cardiovascular risk factors (anthropometric parameters, blood test and blood pressure), b) sedentary and physical activity behaviour and dietary intake, c) psychological aspects d) health related quality of life (HRQOL), e) cost-effectiveness of the intervention in relation to HRQOL. These variables will be then be evaluated 4 times longitudinally: at baseline, at the end of the intervention (8 months later), 6 and 12 months after the intervention. We have considered necessary to recruit 100 children and divide them in 2 groups of 50 to detect the differences between the groups. Discussion: This trial will provide new evidence for the long-term effects of childhood obesity management, as well as help to know the impact of the present intervention as a health intervention tool for healthcare centres. Trial registration: ClinicalTrials.gov, NCT01878994