Post-Traumatic Stress Disorder(PTSD) develops after exposure to or witnessing traumatic events. PTSD is highly comorbid and individuals with PTSD usually report Depressive Symptoms(DS). Common treatment choices for PTSD and DS are either EMDR or CBT, however, little is known about their comparative efficacy, especially in Pakistan. Therefore, this Randomized Controlled Trial(RCT) aims at determining the comparative efficacy of EMDR vs CBT in Pakistan. This study will also examine the association between reduction in symptoms of PTSD and DS over course of treatment. In this regard, two arms Crossover Randomized Controlled Trial(RCT) with Repeated Measures Design will be selected. This study will be conducted at two rehabilitation centers and patients will be screened at Time:01, baseline; Time:02, during treatment; Time:03, post treatment and Time:04, 06 months follow-up. All analyses will be performed according to intention-to-treat principle. Variations in symptoms will be analysed by using descriptive statistics, χ2 tests, t-tests, and one way ANOVA. To examine changes in PTSD and DS across time and to check efficacy of each treatment, a series of Linear Mixed Models will be run. Furthermore, a series of multi-level lagged mediation analysis will be performed to check bi-directional mediation between changes PTSD and DS over time. This protocol has outlined the rationale for determining efficacy of EMDR and CBT in Pakistan. It will help in answering a broad range of questions concerning efficacy of newly developed evidence-based treatments. Moreover, it may also guide future research on the treatment of PTSD and DS in the developing countries.