INTRODUCTION: Sri Lanka has a long history of armed conflict and natural disasters increasing the risk of mental health disorders in the population. Due to a lack of specialist services, there is a treatment gap between those seeking and those able to access mental health services. The aim of this research programme is to integrate mental health services into primary care to meet the needs of this postconflict population. METHODS AND ANALYSIS: This is a stepped wedge cluster design randomised clinical trial of the WHO mental health Gap Action Programme primary care mental health training intervention. We will provide a 10-day training to primary care practitioners of 23 randomly selected primary care facilities aimed at increasing their ability to identify, treat and manage common mental health disorders. Public health professionals and community representatives will receive a tailored training intervention to increase mental health awareness. Refresher courses will occur at 3 and 6 months post training. Supervision and monitoring will occur for 1 month pre and post training. Target sample sizes have been calculated separately for each group of participants and for each outcome. ETHICS AND DISSEMINATION: This trial has received ethical approval from the Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University, UK (SC/jc/FMFREP/16/17 076) and from the Faculty of Medicine, University of Jaffna, Sri Lanka (J/ERC/17/81/NDR/0170) and non-engagement approval has been received from the funding body, the Centers for Disease Control and Prevention (2018-015). All participants gave written consent. Dissemination of study results will be completed through publication of academic articles, conference presentations, town hall meetings, written pamphlets in plain language, reports to Ministry of Health and other government organisations and through social media outlets. TRIAL REGISTRATION NUMBERS: ISRCTN registry: ISRCTN62598070. SLCTR registration number: SLCTR/2018/008.