BACKGROUND: Six key behavioural risk factors (risky alcohol use, smoking, poor diet, physical inactivity, sedentary behaviour and unhealthy sleep patterns) have been identified as strong determinants of chronic disease, such as cardiovascular disease, diabetes and cancers. School-based interventions targeting these multiple health risk behaviours among adolescents have the potential to halt the trajectory towards later disease, whilst online and mobile technology interventions offer advantages in terms of student engagement, reach and scalability. Despite this, the efficacy of eHealth school-based interventions targeting these six health risk behaviours among adolescents has not been evaluated. The proposed systematic review aims to address this by determining the nature and efficacy of existing eHealth school-based interventions targeting multiple health risk behaviours among adolescents. METHODS: A systematic search of the MEDLINE, Embase, PsycINFO and Cochrane Library databases will be conducted to identify eligible published papers. Eligible studies will be randomised controlled trials, including cluster randomised controlled trials, of interventions targeting two or more of the following lifestyle risk behaviours: alcohol use, smoking, poor diet, physical inactivity, sedentary behaviour and sleep. Eligible studies will be those evaluating interventions delivered in a secondary school setting among participants 11-18 years of age, via an eHealth platform (Internet, computers of mobile technology). Two reviewers will independently screen studies for eligibility, extract data and assess the risk of bias. Study outcomes will be summarised in a narrative synthesis, and meta-analyses will be conducted where it is appropriate to combine studies. DISCUSSION: It is anticipated that the results from this review will serve to inform the development of future eHealth multiple health behaviour interventions for adolescents by identifying common characteristics of effective programs and highlighting knowledge gaps in the evidence base. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42017072163.