Refugees and other displaced persons are exposed to many risk factors for unhealthy alcohol and other drug (AOD) use and concomitant mental health problems. Evidence-based services for AOD use and mental health comorbidities are rarely available in humanitarian settings. In high income countries, screening, brief intervention and referral to treatment (SBIRT) systems can provide appropriate care for AOD use but have rarely been used in low- and middle-income countries and to our knowledge never tested in a humanitarian setting. This paper describes the protocol for a randomised controlled trial to compare the effectiveness of an SBIRT system featuring the Common Elements Treatment Approach (CETA) to treatment as usual in reducing unhealthy AOD use and mental health comorbidities among refugees from the Democratic Republic of the Congo and host community members in an integrated settlement in northern Zambia. The trial is an individually randomised, single-blind, parallel design with outcomes assessed at 6-months (primary) and 12-months post-baseline. Participants are Congolese refugees and Zambians in the host community, 15 years of age or older with unhealthy alcohol use. Outcomes are: unhealthy alcohol use (primary), other drug use, depression, anxiety and traumatic stress. The trial will explore SBIRT acceptability, appropriateness, cost-effectiveness, feasibility, and reach.