Abstract Background In humanitarian settings common mental disorders (depression, anxiety disorders, posttraumatic stress disorder) are highly prevalent. The World Health Organization (WHO) has developed Problem Management Plus (PM+), a 5-session, individual psychological intervention program, delivered by paraprofessionals that addresses common mental disorders in people in communities affected by adversity. The objectives of this study are to test effectiveness and cost-effectiveness of the locally adapted PM+ compared to Treatment as usual (TAU) in Peshawar District, Pakistan. Methods A randomised controlled trial will be conducted in 346 primary care attendees in 3 health care centres in Peshawar District, Pakistan. After informed consent, primary care attendees with high levels of psychological distress according to the General Health Questionnaire-12 (GHQ-12) and functional impairment (WHO Disability Assessment Schedule 2.0 (WHODAS)) will be assigned to PM+ (n = 173) or TAU (n = 173). At baseline, 1 week and 3 months following PM+, independent assessors will assess psychological distress with the Hospital Anxiety and Depression Scale (HADS), and functional disability with the WHODAS. Secondary outcomes are posttraumatic stress disorder (PTSD) symptoms, and client-perceived priority problems. Further, cost-effectiveness will be assessed using the Service Receipt Inventory (SRI). Discussion If proven effective, PM+ will be rolled out to other areas for further adaptation and testing in diverse humanitarian settings. Trial registration ACTRN12614001235695 . Registered 26 November 2014. Australian New Zealand Clinical Trials Registry