In this paper a multi-level theoretical and methodological framework for educational neuroscience is presented. The framework incorporates levels of explanation and methodologies both from education and brain sciences. The purpose is to initiate a discussion on the major goals of educational neuroscience as a field, discuss which approaches can provide the ground for a fruitful transdisciplinary fusion of ideas and methods from relevant fields, and propose embodied approaches to cognition as a theoretical scaffold that can amalgamate the multiple levels of inquiry.