Research design and methods in educational neuroscience involve using neuroscientific tools such as brain image technologies to investigate cognitive functions and inform educational practices. The ethical challenges raised by research in social neuroscience have become the focus of neuroethics, a sub-discipline of bioethics. More specifically here, we give an overview of neuroethical issues arising from brain imaging studies and neuropharmacology in education, from neuromyths to potential stigmatization of learners, and discuss the relevance of establishing the field of educational neuroethics. We argue that by integrating ethical positions to research design and methods in educational neuroscience, it would become possible to contextualize results and the diffusion of results, which in turn insure better credibility among the wide variety of stakeholders to new knowledge emerging from educational neuroscience.