A sedentary lifestyle is commonly associated with a higher risk of chronic disease development. Among school-aged children from European countries, screen-time represents a significant portion of sedentary time with 39.8% of children spending more than 2h/day in front of a screen on average. Therefore, effective solutions to reduce sedentary behavior (SB) must be found. Multilevel interventions based on the socio-ecological model (SEM) are particularly relevant to take into account influences of the social environment on individuals' SB. Moreover, the trans-contextual model (TCM) can offer complementary levers for individuals' behavior change. The CIPRES study is a theory-based multilevel intervention designed to decrease the SB in French primary school children aged 8-10 years. The present paper describes the protocol of a randomized controlled study to evaluate the effectiveness of the CIPRES multilevel intervention on SB. The CIPRES study is a cluster-randomized controlled trial comparing intervention vs control groups. A total of 700 children are targeted for inclusion, distributed in four municipalities considered as clusters. The study consists of two successive phases: 1) co-building of a SB prevention intervention by using a participatory approach involving representatives of each level of the SEM (e.g., children, parents, staff from municipalities, teachers) and 2) implementation and evaluation of the intervention. The intervention will last for 6 weeks in each involved class. Primary outcome will be the sedentary time of children per week, assessed by accelerometry. In addition, children and their parents will be asked to fill out questionnaires concerning children's physical activity level, screen time, quality-of-life and variables of the TCM. This study will give information on the effectiveness of a theory-based intervention, involving multiple levels of actors in the co-construction and the implementation of the intervention, that may interest schools and public health officers looking for innovative sedentary prevention programs.