Background This case study describes research, which is located in Turkey, where more than 750,000 Syrian refugees reside autonomously in Istanbul. The research developed and pilot tested a novel model for helping urban refugee families with limited to no access to evidence-based mental health services, by delivering a transdiagnostic family intervention for common mental disorders in health and non-health sector settings using a task-sharing approach. This case study addresses the following question: What challenges were encountered in developing and piloting a low intensity trans-diagnostic family support intervention in a humanitarian emergency setting? Discussion The rapidly growing scale of humanitarian crises requires new response capabilities geared towards addressing populations with prolonged high vulnerability to mental health consequences and limited to no access to mental health, health, and social resources. The research team faced multiple challenges in conducting this research in a humanitarian emergency setting including: 1) Non-existent or weak partnerships geared towards mental health research in a humanitarian emergency; 2) Lack of familiarity with task-sharing; 3). Insufficient language and cultural competency; 3) Fit with families' values and demands; 4) Hardships of urban refugees. Through the research process, the research team learned lessons concerning: 1) building a coalition of academic and humanitarian organization partners; 2) investing in the research capacity building of local researchers and partners; 3) working in a community-collaborative and multi-disciplinary approach. Conclusion Conducting research in humanitarian emergency settings calls for innovative collaborative and multidisciplinary approaches to understanding and addressing many sociocultural, contextual, practical and scientific challenge.