Abstract: There are high rates of posttraumatic stress disorder (PTSD) among treatment-seeking veterans with substance use disorders (SUD). While addiction programs traditionally do not address PTSD, there is evidence that trauma treatments for individuals with this comorbidity have improved PTSD and SUD outcomes. Written exposure therapy (WET), a five-session evidence-based psychotherapy (EBP) for PTSD, has high patient satisfaction, and lower dropout compared to other EBPs for PTSD. WET may be ideally suited for clinical settings that may not have the trauma expertise found in PTSD specialty clinics, given it requires less training time, treatment sessions, preparation time, and therapist involvement than existing EBPs, and no homework assignments. This paper describes the design, methodology, and protocol of a randomized clinical trial to evaluate whether treatment as usual (TAU) plus WET (n = 51) is superior to TAU plus a neutral topic writing condition (n = 51) on both PTSD and addiction outcomes for veterans in SUD treatment. The primary hypothesis is that participants assigned to TAU+WET, compared to those in TAU+ neutral topic writing, will report reduced symptoms of PTSD. The secondary hypothesis is that veterans receiving WET will have greater decreases in number of days of substance use compared to TAU+ neutral topic controls at follow-up. Assessments will take place at baseline, post-treatment, 8-week, and 12-week follow-up. Exploratory aims will examine the association between heart rate variability and treatment outcomes. If results prove promising, they will support WET as an effective brief, easy to disseminate, adjunct to current SUD treatment for veterans with comorbid PTSD.