BACKGROUND: Inadequacy in mental health care in low and middle income countries has been an important contributor to the rising global burden of disease. The treatment gap is salient in resource-poor settings, especially when providing care for conflict-affected forced migrant populations. Primary care is often the only available service option for the majority of forced migrants, and integration of mental health into primary care is a difficult task. The proposed pilot study aims to explore the feasibility of integrating mental health care into primary care by providing training to primary care practitioners serving displaced populations, in order to improve identification, treatment, and referral of patients with common mental disorders via the World Health Organization Mental Health Gap Action Programme (mhGAP). METHODS/DESIGN: This pilot randomized controlled trial will recruit 86 primary care practitioners (PCP) serving in the Puttalam and Mannar districts of Sri Lanka (with displaced and returning conflict-affected populations). The intervention arm will receive a structured training program based on the mhGAP intervention guide. Primary outcomes will be rates of correct identification, adequate management based on set criteria, and correct referrals of common mental disorders. A qualitative study exploring the attitudes, views, and perspectives of PCP on integrating mental health and primary care will be nested within the pilot study. An economic evaluation will be carried out by gathering service utilization information. DISCUSSION: In post-conflict Sri Lanka, an important need exists to provide adequate mental health care to conflict-affected internally displaced persons who are returning to their areas of origin after prolonged displacement. The proposed study will act as a local demonstration project, exploring the feasibility of formulating a larger-scale intervention study in the future, and is envisaged to provide information on engaging PCP, and data on training and evaluation including economic costs, patient recruitment, and acceptance and follow-up rates. The study should provide important information on the WHO mhGAP intervention guide to add to the growing evidence base of its implementation. TRIAL REGISTRATION: SLCTR/2013/025.