2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This article presents a case study of research in Dadaab, Kenya to highlight some of the relevant challenges encountered while conducting gender-based violence research in humanitarian settings. A longitudinal mixed-methods design was used to evaluate a comprehensive case-management intervention in the refugee complex near the border of Kenya and Somalia. We present an overview of both expected and unexpected challenges during preparation and implementation of the research, adaptations made to the research design, and lessons learned for future research in similar contexts. Some of the key challenges were attributed to the highly securitized and remote environment of Dadaab refugee camp, like many refugee camp settings, which created limitations for sampling designs, interview locations, and also created particular burdens for the research team members conducting interviews. In addition to the camp environment, the dynamic nature of events and trends in the camp setting created barriers to follow-up with longitudinal cohort participants as well as uncertainty on how to plan for future implementation of research design phases in response to camp changes. Conducting research in humanitarian settings requires a flexible approach to accommodate the challenges that can impact both service delivery and research activities. The discussion presented in this article contributes to the evolving practical guidance on conducting research in humanitarian settings.