Background: Millions of children worldwide suffer from posttraumatic stress disorder (PTSD) symptoms and other mental health problems due to repeated exposure to war or organized violence. Forms of cognitive-behavioral therapy (CBT) are the most commonly used treatment for PTSD and appear to be effective for children as well, but little is known about the mechanisms of change through which they achieve their effectiveness. Here we present the study protocol of a randomized controlled trial (RCT) studying the effectiveness and mechanisms of change of Narrative Exposure Therapy (NET), a CBT-based, manualized, short-term intervention for PTSD symptoms resulting from repeated traumatization, in immigrant children traumatized by war. Methods/Design: We are conducting a multicentre, pragmatic RCT in a usual care setting. Up to 80 9-17-year-old immigrant children who have experienced war and suffer from PTSD symptoms will be randomized into intervention (NET) and control (treatment as usual, TAU) groups of equal sizes. The effectiveness of NET treatment will be compared to both a waiting list and the parallel TAU positive control group, on the primary outcomes of PTSD and depressive symptoms, psychological distress, resilience, and level of cognitive performance. The effects of the intervention on traumatic memories and posttraumatic cognitions will be studied as potential mechanisms of change mediating overall treatment effectiveness. The possible moderating effects of peritraumatic dissociation, level of cognitive performance, and gender on treatment effectiveness will also be considered. We hypothesize that NET will be more effective than a waitlist condition or TAU in reducing PTSD and other symptoms and improving resilience, and that these effects will be mediated by changes in traumatic memories and posttraumatic cognitions. Discussion: The results of this trial will provide evidence for the effectiveness of NET in treating trauma-related symptoms in immigrant children affected by war. The trial will also generate insights into the complex relationships between PTSD, memory functions, posttraumatic cognitions and cognitive performance in children, and help guide the future development and implementation of therapeutic interventions for PTSD in children.