Abstract Background The World Health Organization (WHO) has developed Problem Management Plus (PM+), a 5-session, psychological intervention program delivered by trained non-specialist that addresses common mental disorders. The objectives of this study are to evaluate effectiveness and cost-effectiveness of PM+ in a specialized mental health care facility in Pakistan. Methods A single blind individual randomized controlled trial (RCT) will be carried out in the outpatient department of a specialized mental healthcare facility in Rawalpindi, Pakistan. After informed consent, patients with high psychological distress (General Health Questionnaire-12 (score >2) and functional impairment (WHO Disability Assessment Schedule 2.0 score >16) will be randomised to PM+ plus treatment as usual (n = 96) or TAU only (n = 96). The primary outcome is the psychological distress, measured by levels of anxiety and depression on the Hospital Anxiety and Depression Scale and improvement in functioning as measured by WHODAS at 20 weeks after baseline. Secondary outcomes include improvement in symptoms of depression, post-traumatic stress disorder, levels of social support and cost effectiveness evaluation. Qualitative interviews will be conducted to evaluate the process of implementing PM+ including barriers and facilitators in implementation and possibility of integration of PM+ program in specialized mental health care facilities in Pakistan. Discussion The results of this study will be helpful in evaluating the effectiveness of the approach of training non specialists, based in the specialized mental health care facilities in delivering evidence based psychological interventions in the low resource settings. Trial registration Australian New Zealand Clinical Trials Registry, ACTRN12616000381482. Registered Retrospectively on March 23, 2016