Background Populations affected by humanitarian emergencies are vulnerable to substance (alcohol and other drug) use disorders, yet treatment and prevention services are scarce. Delivering substance use disorder treatment services in humanitarian settings is hampered by limited guidance around the preparation, implementation, and evaluation of substance use disorder treatment programs. This study aims to identify and prioritize key gaps and opportunities for addressing substance use disorder in humanitarian settings. Methods UNODC convened a consultation meeting (n = 110) in coordination with UNHCR and WHO and administered an online survey (n = 34) to, thirteen program administrators and policymakers, eleven service providers, nine researchers, and one person with lived experience to explore best practices and challenges to addressing substance use disorder in diverse populations and contexts. Participants presented best practices for addressing substance use disorder, identified and ranked challenges and opportunities for improving the delivery of substance use disorder treatment interventions, and provided recommendations for guidelines that would facilitate the delivery of substance use disorder treatment services in humanitarian emergencies. Results Participants agreed on key principles for delivering substance use disorder treatment in humanitarian settings that centered on community engagement and building trust, integrated service delivery models, reducing stigma, considering culture and context in service delivery, and an ethical 'do no harm' approach. Specific gaps in knowledge that precluded the delivery of appropriate substance use disorder treatment include limited knowledge of the burden and patterns of substance use in humanitarian settings, the effectiveness of substance use disorder treatment services in humanitarian settings, and strategies for adapting and implementing interventions for a given population and humanitarian context. Participants emphasized the need to strengthen awareness and commitment related to the burden of substance use disorder treatment interventions among communities, practitioners, and policymakers in humanitarian settings. Conclusions Results from this consultation process highlight existing gaps in knowledge related to the epidemiology and treatment of substance use disorders in humanitarian emergencies. Epidemiological, intervention, and implementation research as well as operational guidance are needed to fill these gaps and improve access to substance use treatment services in humanitarian settings.