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Introduction The treatment of comorbid post-traumatic stress disorder (PTSD) and alcohol use disorder (AUD) is significantly more challenging than the treatment of either disorder alone. While gold standard evidence-based treatments exist for this comorbidity, clinically significant improvements are only observed in approximately half of clinical trial participants. The use of adjunctive pharmacotherapies, such as 3,4-methylenedioxymethamphetamine (MDMA), may serve to optimise gold standard interventions. The primary aim of the MDMA-assisted PTSD and Alcohol Therapy Trial study is to examine the therapeutic and cost-effectiveness of combining MDMA with evidence-based integrated care for comorbid PTSD+AUD. Specifically, we will examine MDMA-assisted integrated exposure therapy versus active control-assisted integrated exposure therapy in improving treatment outcomes for PTSD+AUD.Methods and analysis This world-first double-blind trial will aim to randomise 100 participants with PTSD+AUD to a regimen of Concurrent Treatment of PTSD and Substance Use Disorders Using Prolonged Exposure (COPE) (12 sessions)+MDMA (80–160 mg: 2 dosing and 2 integration sessions) or COPE (12 sessions)+active control (niacin 250 mg: 2 dosing sessions and 2 integration sessions). All participants will receive medical management. The primary PTSD outcome will be the clinician-administered PTSD Scale for DSM-5. The primary drinking outcome will be the number of heavy drinking days (HDDs) per week, validated by phosphatidylethanol. Secondary PTSD and alcohol-related outcomes will include PTSD checklist for DSM-5 scores, absence of any HDDs and standard drinks per drinking day. We will also examine change in other clinical conditions and symptoms including depression, sleep disturbances and post-traumatic cognitions; treatment satisfaction and engagement; adverse events; and cost-effectiveness.Ethics and dissemination This study will be conducted in accordance with the ethical principles outlined in the Declaration of Helsinki and the International Conference on Harmonisation-Good Clinical Practice guidelines. Ethical approval has been granted by the Sydney Local Health District Ethics Review Committee (X22-0121 & 2022/ETH00773). The results of this study will provide world-first data regarding safety, efficacy and cost-effectiveness of MDMA to optimise integrated exposure-based therapy for comorbid AUD and PTSD and will be disseminated to ensure wide accessibility and to support further research and clinical application.Trial registration number NCT05709353.