Abstract Background Childhood overweight has noticeable psychological and social consequences for the child and leads to an increased risk of mortality and morbidity later in life. With the high prevalence of overweight in children and adolescents, it is important to identify effective approaches for the prevention and treatment of overweight in children and young individuals. The primary aim of the study is to assess the effect of an intensive day-camp intervention on body mass index (BMI) in overweight children. Methods The Odense Overweight Intervention Study is a semi-blinded randomized controlled trial. Overweight children from the Municipality of Odense, Denmark, were invited to participate in the trial. Based on power calculations 98 participants were found to be sufficient to randomize in order to find an effect of minimum 1.5 BMI points. Gender-stratified concealed block randomization with a ratio of 1:1 and random block sizes of two, four, and six ensured balance between study arms. The intervention consisted of a six-week multi-component day camp including increased physical activity, healthy diet and health education followed by 46 weeks of family-based habitual intervention. The standard care arm was offered two weekly hours of physical activity training for six weeks. The outcomes were measured at baseline and at six-week and 52-week follow-ups. Furthermore, BMI will be assessed again at 48-month follow-up. Test personnel were kept blinded. The intervention effect will be evaluated using mixed model analyses. During 2012 and 2013, 115 children were enrolled in the study. Fifty-nine children were randomized to the day-camp intervention arm and 56 to the standard intervention arm. Discussion This study will provide novel information about the long-term health effects of an intense day-camp intervention program on overweight children, due to the design and the follow-up period. Moreover, it will add to the knowledge on designing and implementing feasible camp settings for preventing overweight in children. Trial registration NCT01574352 at http://clinicaltrials.gov on the 8th of March 2012.