Background: Eye Movement Desensitization and Reprocessing (EMDR) is an evidence-based treatment for PTSD. However, it is unclear whether EMDR shows the same effectiveness in patients with substance use disorders (SUD) and comorbid PTSD. In this trial, we examine the effectiveness of EMDR in reducing PTSD symptoms in patients with SUD and PTSD. Methods/Design: We conduct a single-blinded RCT among 158 patients with SUD and comorbid PTSD admitted to a German addiction rehabilitation center specialized for the treatment of patients with SUD and comorbid PTSD. Patients are randomized to receive either EMDR, added to SUD rehabilitation and non-trauma-focused PTSD treatment (TAU), or TAU alone. The primary outcome is change from baseline in PTSD symptom severity as measured by the ClinicianAdministered PTSD Scale at 6-month follow-up. Secondary outcomes are change from baseline in substance use, addiction-related problems, depressive symptoms, dissociative symptoms, emotion dysregulation and quality of life. Assessments are carried out by blinded raters at admission, at end of treatment, and at 3- and 6-month follow-up. We expect that EMDR plus TAU will be more effective in reducing PTSD symptoms than TAU alone. Mixed models will be conducted using an intention-to-treat and per-protocol approach. Discussion: This study aims to expand the knowledge about the effectiveness of EMDR in patients with SUD and comorbid PTSD. The expected finding of the superiority of EMDR in reducing PTSD symptoms compared to non-trauma-focused PTSD treatment may enhance the use of trauma-focused treatment approaches for patients with SUD and co-morbid PTSD.