Background: Treatment of traumatised refugees is one of the fields within psychiatry, which has received little scientific attention. Evidence based treatment and knowledge on the efficiency of the treatment for this complex patient group is therefore scarce. This leads to uncertainty as to which treatment should be offered and potentially lowers the quality of life for the patients. Chronic pain is very common among traumatised refugees and it is believed to maintain the mental symptoms of trauma. Hence, treating chronic pain is believed to be of high clinical value for this patient group. In clinical studies, physical activity has shown a positive effect on psychiatric illnesses such as depression and anxiety and for patients with chronic pain. However, scientific knowledge about physical activity as part of the treatment for traumatised refugees is very limited and no guidelines exist on this topic. Methods/design: This study will include approximately 310 patients, randomised into three groups. All three groups receive psychiatric treatment as usual for the duration of 6-7 months, consisting of consultations with a medical doctor including pharmacological treatment and manual-based Cognitive Behavioural Therapy. The first group only receives treatment as usual while the second and the third groups receive either Basic-Body Awareness Therapy or mixed physical activity as add-on treatments. Each physical activity is provided for an individual 1-hour consultation per week, for the duration of 20weeks. The study is being conducted at the Competence Centre for Transcultural Psychiatry, Mental Health Centre Ballerup in the Capital Region of Denmark. The primary endpoint of the study is symptoms of Post Traumatic Stress Disorder; the secondary endpoints are depression and anxiety as well as quality of life, functional capacity, coping with pain, body awareness and physical fitness. Discussion: This study will examine the effect of physical activity for traumatised refugees. This has not yet been done in a randomised controlled setting on such a large scale before. Hereby the study will contribute to important knowledge that is expected to be used in future clinical guidelines and reference programs. Trial registration: ClinicalTrials.gov NCT01955538. Date of registration: 18 September 2013.