INTRODUCTION: Post-traumatic stress disorder (PTSD) is a debilitating, highly prevalent condition. Current clinical practice guidelines recommend trauma-focused psychotherapy (eg, cognitive processing therapy; CPT) as the first-line treatment for PTSD. However, while these treatments show clinically meaningful symptom improvement, the majority of those who begin treatment retain a diagnosis of PTSD post-treatment. Perhaps for this reason, many individuals with PTSD have sought more holistic, mind-body, complementary and integrative health (CIH) interventions. However, there remains a paucity of high-quality, active controlled efficacy studies of CIH interventions for PTSD, which precludes their formal recommendation.METHODS AND ANALYSES: We present the protocol for an ongoing non-inferiority parallel group randomised controlled trial (RCT) comparing the efficacy of a breathing meditation intervention (Sudarshan Kriya Yoga [SKY]) to a recommended evidence-based psychotherapy (CPT) for PTSD among veterans. Assessors are blinded to treatment group. The primary outcome measure is the PTSD Checklist-Civilian Version and a combination of clinical, self-report, experimental and physiological outcome measures assess treatment-related changes across each of the four PTSD symptom clusters (re-experiencing, avoidance, negative cognitions or mood and hyperarousal/reactivity). Once the RCT is completed, analyses will use both an intent-to-treat (using the 'last observation carried forward' for missing data) and a per-protocol or 'treatment completers' procedure, which is the most rigorous approach to non-inferiority designs. ETHICS AND DISSEMINATION: To the best of our knowledge, this is this first non-inferiority RCT of SKY versus CPT for PTSD among veterans. The protocol is approved by the Stanford University Institutional Review Board. All participants provided written informed consent prior to participation. Results from this RCT will inform future studies including larger multi-site efficacy RCTs of SKY for PTSD and other mental health conditions, as well as exploration of cost-effectiveness and evaluation of implementation issues. Results will also inform evidence-based formal recommendations regarding CIH interventions for PTSD. TRIAL REGISTRATION NUMBER: NCT02366403; Pre-results.