Background Young men are consistently less likely to seek help for mental health problems than their female peers. This is particularly concerning given the high rates of suicide among male adolescents. The school system has been identified as an ideal setting for the implementation of prevention and early intervention programs for young people. The current trial aims to determine the effectiveness of the Silence is Deadly program in increasing positive help-seeking intentions for mental health problems and suicide among male secondary school students. Methods This study is a two-arm, cluster-randomised, controlled trial that will compare the Silence is Deadly program to a wait-list control condition. Eight Australian high schools will be recruited to the trial, with male students in grades 11 and 12 (16 to 18 years of age) targeted for participation. The program is an innovative male-tailored suicide prevention intervention, comprising a presentation that emphasises role-modelling and legitimises help-seeking for personal and emotional problems, and a brief video that features celebrity athletes who counter existing male norms around help-seeking and encourage communication about personal and emotional issues. The program also includes a discussion of how to help a friend in distress and ends with a question and answer session. The primary outcome measure for the current study is help-seeking intentions. Secondary outcomes include help-seeking behaviour, help-seeking attitudes, help-seeking stigma, mental health symptoms, and suicidal ideation. Data will be collected pre-intervention, post-intervention, and at 3-month follow-up. Primary analyses will compare changes in help-seeking intentions for the intervention condition relative to the wait-list control condition using mixed-effects repeated-measures analyses that account for clustering within schools. Discussion If proven to be effective, this targeted help-seeking intervention for adolescent males, which is currently only delivered in one jurisdiction, could be more widely delivered in Australian high schools. The Silence is Deadly program has the potential to significantly contribute to the mental health of young men in Australia by improving help-seeking for suicidality and mental health problems, allowing this population to better access treatment and support sooner. Trial registration Australian New Zealand Clinical Trials Registry, ACTRN12617000658314. Registered on 8 May 2017. Electronic supplementary material The online version of this article (10.1186/s12889-017-4845-z) contains supplementary material, which is available to authorized users.