BACKGROUND: Anxiety and depression are associated with a range of adverse outcomes and represent a large global burden to individuals and health care systems. Prevention programs are an important way to avert a proportion of the burden associated with such conditions both at a clinical and subclinical level. eHealth interventions provide an opportunity to offer accessible, acceptable, easily disseminated globally low-cost interventions on a wide scale. However, the efficacy of these programs remains unclear. The aim of this study is to review and evaluate the effects of eHealth prevention interventions for anxiety and depression. METHOD: A systematic search was conducted on four relevant databases to identify randomized controlled trials of eHealth interventions aimed at the prevention of anxiety and depression in the general population published between 2000 and January 2016. The quality of studies was assessed and a meta-analysis was performed using pooled effect size estimates obtained from a random effects model. RESULTS: Ten trials were included in the systematic review and meta-analysis. All studies were of sufficient quality and utilized cognitive behavioural techniques. At post-treatment, the overall mean difference between the intervention and control groups was 0.25 (95% confidence internal: 0.09, 0.41; p = 0.003) for depression outcome studies and 0.31 (95% CI: 0.10, 0.52; p = 0.004) for anxiety outcome studies, indicating a small but positive effect of the eHealth interventions. The effect sizes for universal and indicated/selective interventions were similar (0.29 and 0.25 respectively). However, there was inadequate evidence to suggest that such interventions have an effect on long-term disorder incidence rates. CONCLUSIONS: Evidence suggests that eHealth prevention interventions for anxiety and depression are associated with small but positive effects on symptom reduction. However, there is inadequate evidence on the medium to long-term effect of such interventions, and importantly, on the reduction of incidence of disorders. Further work to explore the impact of eHealth psychological interventions on long-term incidence rates.