In its origins educational neuroscience has started as an endeavor to discuss implications of neuroscience studies for education. However, it is now on its way to become a transdisciplinary field, incorporating findings, theoretical frameworks and methodologies from education, and cognitive and brain sciences. Given the differences and diversity in the originating disciplines, it has been a challenge for educational neuroscience to integrate both theoretical and methodological perspective in education and neuroscience in a coherent way. We present a multi-level framework for educational neuroscience, which argues for integration of multiple levels of analysis, some originating in brain and cognitive sciences, others in education, as a roadmap for the future of educational neuroscience with concrete examples in moral education.