BACKGROUND: Schools provide a natural context to promote children’s mental health. However, there is a need for more evidence-based, high quality school intervention programs combined with an accurate evaluation of their general effectiveness and effectiveness of specific intervention methods. The aim of this paper is to present a study protocol of a cluster randomized controlled trial evaluating the ‘Together at School’ intervention program. The intervention program is designed to promote social-emotional skills and mental health by utilizing whole-school approach and focuses on classroom curriculum, work environment of school staff, and parent-teacher collaboration methods. METHODS/DESIGN: The evaluation study examines the effects of the intervention on children’s socio-emotional skills and mental health in a cluster randomized controlled trial design with 1) an intervention group and 2) an active control group. Altogether 79 primary school participated at baseline. A multi-informant setting involves the children themselves, their parents, and teachers. The primary outcomes are measured using parent and teacher ratings of children’s socio-emotional skills and psychological problems measured by the Strengths and Difficulties Questionnaire and the Multisource Assessment of Social Competence Scale. Secondary outcomes for the children include emotional understanding, altruistic behavior, and executive functions (e.g. working memory, planning, and inhibition). Secondary outcomes for the teachers include ratings of e.g. school environment, teaching style and well-being. Secondary outcomes for both teachers and parents include e.g. emotional self-efficacy, child rearing practices, and teacher-parent collaboration. The data was collected at baseline (autumn 2013), 6 months after baseline, and will be collected also 18 months after baseline from the same participants. DISCUSSION: This study protocol outlines a trial which aims to add to the current state of intervention programs by presenting and studying a contextually developed and carefully tested intervention program which is tailored to fit a national school system. Identification of effective intervention elements to promote children’s mental health in early school years is crucial for optimal later development. TRIAL REGISTRATION: ClinicalTrials.gov register: NCT02178332.