In recent years, educational neuroscience has begun to move into the limelight, suggesting an increased importance on the ethical considerations of educational neuroscience work, or educational neuroethics. In a departure from previous work on educational neuroethics, this article focuses on the ethical considerations that are applicable to empirical educational neuroscience research. Neuroethics concepts were compiled through a thorough survey of neuroethics articles. Then, 28 empirical educational neuroscience articles were analyzed through the lens of five categories of neuroethics concepts collected through the literature survey: the scientific enterprise, prediction, neuro-manipulation, social considerations, and philosophical considerations. Three of the five categories (i.e., the nature of scientific investigation, prediction, and social considerations) applied to a subset of the articles. In addition, a fourth ethical issue not stemming from the neuroethics literature, referred to here as brain-based justifications, emerged from the nature of educational neuroscience work. Limitations of this study and future directions for educational neuroethics research are discussed.