Evidence is mounting that nature-based learning (NBL) enhances children’s educational and developmental outcomes, making this an opportune time to identify promising questions to carry research and practice in this field forward. We present the outcomes of a process to set a research agenda for NBL, undertaken by the Science of Nature-Based Learning Collaborative Research Network, with funding from the National Science Foundation. A literature review and several approaches to gathering input from researchers, practitioners and funders resulted in recommendations for research questions and methodological improvements to increase the relevance and rigor of research in this field. Some questions seek to understand how learning in nature affects what children learn, how they learn, and how it varies based on age, gender, socioeconomic status, ethnic background, special needs and individual differences. Outcomes of interest cover academic performance, practical skills, personal development, and environmental stewardship. Other questions seek to find causal explanations for observed outcomes. To create optimal conditions for NBL, the research agenda includes practical questions about how to prepare teachers to work successfully in nature and how to support their adoption of this approach. Not least, the research agenda asks whether learning in nature can address major societal issues by moderating the effect of socioeconomic disadvantage on children’s academic achievement, personal development and wellbeing, and how these benefits might be attained at reasonable costs. A deeper understanding of how, why and for whom different forms of nature contact enhance learning and development is needed to guide practice and policy decision-making.