Background. Lifetime trajectories of mental ill health are often established during adolescence. Effective interventions to prevent the emergence of mental health problems are needed. In the current study we assessed the efficacy of the CBT informed Climate Schools universal eHealth preventive mental health program, relative to a control. We also explored whether the intervention had differential effects on students with varying degrees of social connectedness. Method. We evaluated the efficacy of the Climate Schools mental health program (19 participating schools; average age at baseline was 13.6) versus an active control group (18 participating schools; average age at baseline was 13.5) which formed part of a large cluster randomised controlled trial in Australian schools. Measures of internalising problems, depression and anxiety were collected at baseline, immediately following the intervention and at 6-, 12- and 18-months post intervention. Immediately following the intervention, 2539 students provided data on at least one outcome of interest (2065 students at 18 months post intervention). Results. We found no evidence that the stand-alone mental health intervention improved outcomes, on any measure, relative to a control. Across all participants we observed small, but significant, increases in internalising problems, depression, and anxiety at 18 months post intervention, relative to baseline. Student’s social connectedness did not influence intervention outcomes. Conclusion. These results are consistent with recent findings that universal school-based, CBT informed, preventive interventions for mental health have limited efficacy when delivered alone. We highlight the potential for combined intervention approaches, and more targeted interventions, to better improve outcomes.