The transition from childhood to adolescence often elicits psychological problems, which provides great opportunities for organizing universal, school-based prevention programs. The present study aims to evaluate the effectiveness of Boost Camp, a new prevention program targeting young adolescents’ emotion regulation skills. Junior high school adolescents (n = 347; 53% female, Mage = 11.92) from six schools were randomly allocated to the intervention condition (n = 139) or to the control condition (n = 208), using a clustered randomized controlled design. Program integrity was evaluated by adolescents, trainers, and independent coders. Questionnaires were used to assess primary outcomes (emotion regulation and emotional wellbeing), secondary outcomes (school achievement, bullying experiences, and psychological stigmatization), and moderators (gender, psychological problems, and executive functioning). Assessment of the main outcome variables was conducted at baseline, post intervention, and three as well as six months’ follow-up. Qualitative analyses showed a good program adherence and positive evaluations of the program. Furthermore, main results demonstrated that Boost Camp had short-term effects on depressive symptoms, self-esteem, indirect bullying experiences, and psychological stigmatization. However, no significant effects on emotion regulation were found and all beneficial effects immediately after the intervention disappeared at follow-up. Program effects were not moderated by gender, executive functioning impairments, or symptoms of psychopathology. These findings demonstrate that Boost Camp is feasible as a universal, school-based program and that it has the potential to enhance wellbeing outcomes, at least short-term and when implemented by external trainers. Several suggestions to optimize the program in order to obtain long-term effects are included in the discussion section.