BackgroundSubstance misuse, including problematic drug and alcohol use, are significant issues in society that can have multiple detrimental effects. Many people access support for their substance misuse during prison sentences, due to the associations between substance misuse and offending, and the high proportion of the prison population who have drug and alcohol issues. Breaking Free Online Health and Justice is a computer-assisted therapy program that has been developed to support substance-involved offenders to address their substance misuse and associated offending within prison settings.MethodsThis will be a parallel-group randomized controlled trial of 4-week Breaking Free Online Health and Justice program as an adjunct to standard treatment for substance misuse, in comparison to standard treatment only, in a male Category D open prison. Interventional and control groups will be compared in terms of the changes in their scores on multiple measures from baseline to post-treatment assessment at 4-weeks, and then 3- and 6-months follow-up. Participants will be adult male offenders serving sentences in prison in England who have demonstrable difficulties with drugs and/or alcohol for at least the past 12-months. The primary outcome measure will be self-reported substance misuse, with secondary outcomes being standardized psychometric assessments of substance dependence, mental health, biopsychosocial functioning, quality of life and post-release offending. Other secondary measures will include frequency of completion of specific intervention strategies in the program.DiscussionThis study will examine whether Breaking Free Online Health and Justice as an adjunct to standard substance misuse interventions in prisons, improves outcomes for substance-involved offenders receiving interventions in custodial settings. Findings from the study will be used to inform further developments of the program and potential improvements to custodial treatment.Trials registrationISRCTN09846981.Electronic supplementary materialThe online version of this article (10.1186/s40352-018-0078-1) contains supplementary material, which is available to authorized users.