Background: Mental health problems are a significant social issue that have multiple consequences, including broad social and economic impacts. However, many individuals do not seek assistance for mental health problems. Limited research suggests martial arts training may be an efficacious sports-based mental health intervention that potentially provides an inexpensive alternative to psychological therapy. Unfortunately, the small number of relevant studies and other methodological problems lead to uncertainty regarding the validity and reliability of existing research. This study aims to examine the efficacy of a martial arts based therapeutic intervention to improve mental health outcomes. Methods/design: The study is a 10-week secondary school-based intervention and will be evaluated using a randomised controlled trial. Data will be collected at baseline, post-intervention, and 12-week follow-up. Power calculations indicate a maximum sample size of n = 293 is required. The target age range of participants is 11–14 years, who will be recruited from government and catholic secondary schools in New South Wales, Australia. The intervention will be delivered in a face-to-face group format onsite at participating schools and consists of 10 × 50–60 min sessions, once per week for 10 weeks. Quantitative outcomes will be measured using standardised psychometric instruments. Discussion: The current study utilises a robust design and rigorous evaluation process to explore the intervention’s potential efficacy. As previous research examining the training effects of martial arts participation on mental health outcomes has not exhibited comparable scale or rigour, the findings of the study will provide valuable evidence regarding the efficacy of martial arts training to improve mental health outcomes. Trial registration: Australian New Zealand Clinical Trials Register ACTRN12618001405202. Registered 21st August 2018.