Background: While the evidence base for cash transfer programming (CTP) in humanitarian contexts is more established for food security, it is very limited for health and nutrition. The aim of this study was to develop a research agenda on CTP for health and nutrition in humanitarian settings. Methods: This exercise adopted a qualitative descriptive approach using four stages over a 13-month period (October 2016 to November 2017). Data was collected using two methods: an online survey and face-to-face group session. The advisory group was asked to judge questions based on four criteria (answerability/feasibility, fills important knowledge gap, maximum potential for improving health or nutrition outcomes, effect on equity) using a 5-point scale. Content analysis was used to identify and rank research categories. Results: One hundred eighty-nine research questions were developed in the consultation stage (n = 40 online survey; n = 30 group session), which were categorised into nine overarching research areas (with 22 sub-categories): modalities (41% of the identified questions), followed by outcomes and impact (31%), intermediate outcomes (27%) , initial considerations (19%), effectiveness (19%), pathways (14%), methodologies and indicators (13%), types of diseases or health issues (6%), and context (5%). Triangulation with other evidence reviews confirmed the need for further research in these areas. Conclusions: Nine overarching and ranked categories for research on CTP for health and nutrition in humanitarian contexts, validated by existing reviews, are proposed by this study. The research agenda, with examples of questions, could serve as guidance for researchers, policy-makers, implementers, and funders when selecting which of the many gaps in the current evidence base on this topic to start addressing first.