Introduction Transdiagnostic cognitive-behavioural therapy (CBT) targets common psychological factors that underlie multiple disorders. While transdiagnostic interventions are a promising new approach, limited research has evaluated these treatments within the alcohol and other drug (AOD) sector for young people with comorbid mental health symptoms. This project will examine the feasibility and preliminary efficacy of FullFix - a new risk-targeted transdiagnostic CBT telehealth programme for comorbid AOD and depression/anxiety disorders in young people. Secondary aims are to identify moderators and mediators of treatment outcomes, to determine how and why treatment is effective and who is most likely to benefit. Methods/design Participants will be 130 young people (aged 16-35) accessing AOD services in Queensland, Australia, with comorbid mental health symptoms. They will be randomised to receive either the FullFix intervention plus standard AOD care or standard AOD care alone. Primary outcomes on AOD use and mental health symptoms will be reassessed at 6 weeks, 3 months, 6 months and 12 months, along with secondary outcomes of emotion regulation, social connectedness, perceived self-efficacy, coping skills and quality of life. The trial commenced on October 2018 and expected completion date is September 2021. Ethics and dissemination Ethical approval for this trial was provided by the University of Queensland (#2018001185). The results of the trial will be disseminated through publication in a peer-reviewed scientific journal, scientific presentations at conferences and distributed via a report and presentations to the partner organisation. Trial registration number ACTRN12618001563257.