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Abstract Background Suicide is a leading cause of death among adolescents in North America. Youth who present to the Emergency Department (ED) with acute suicidality are at increased risk for eventual death by suicide, thereby presenting an opportunity for secondary prevention of suicide. The current study evaluates the effectiveness of a standardized individual and family-based suicidal behaviour risk reduction intervention targeting adolescents at high-risk for suicide. Methods A randomized controlled trial (RCT) will be conducted to evaluate the effectiveness of a manualized youth- and family- based suicide prevention strategy (SPS) as compared with case navigation (NAV) among adolescents aged 12 to 18 years of age who present to the ED with acute suicidal ideation (SI) or suicide risk behaviours (SRB). We will recruit 128 participants and compare psychiatric symptoms including SI/SRB, family communication, and functional impairment at baseline and follow-ups (post-intervention [6 weeks], 24 weeks). The primary outcome is change in suicidal ideation measured with the Suicide Ideation Questionnaire- Junior. SRBs are measured with the Suicide Behaviour Questionnaire. Secondary outcomes are change in depressive and anxious symptoms measured with semi-structured psychiatric interview and Screen for Child Anxiety Related Disorders; acute mental health crises measured by urgent medical (including ED) visits; family communication measured with Conflict Behaviour Questionnaire, functional impairment measured by Columbia Impairment Scale; cost effectiveness, and fidelity of implementation measured by audio recording and fidelity checklist. Discussion Results of this study will inform a larger multi-centre RCT that will include both community and academic hospitals in urban and rural settings. Study results will be shared at international psychiatry and emergency medicine meetings, in local rounds, and via publication in academic journals and clinician-oriented newsletters. If effective, the intervention may provide a brief, scalable, and transportable treatment program that may be implemented in a variety of settings, including those in which access to children’s mental health care services is challenging. Trial registration ClinicalTrials.gov: NCT03488602, retrospectively registered April 4, 2018.