Metacognition comprises both the ability to be aware of one’s cognitive processes (metacognitive knowledge) and to regulate them (metacognitive control). Research in educational sciences has amassed a large body of evidence on the importance of metacognition in learning and academic achievement. More recently, metacognition has been studied from experimental and cognitive neuroscience perspectives. This research has started to identify brain regions that encode metacognitive processes. However, the educational and neuroscience disciplines have largely developed separately with little exchange and communication. In this article, we review the literature on metacognition in educational and cognitive neuroscience and identify entry points for synthesis. We argue that to improve our understanding of metacognition, future research needs to (i) investigate the degree to which different protocols relate to the similar or different metacognitive constructs and processes, (ii) implement experiments to identify neural substrates necessary for metacognition based on protocols used in educational sciences, (iii) study the effects of training metacognitive knowledge in the brain, and (iv) perform developmental research in the metacognitive brain and compare it with the existing developmental literature from educational sciences regarding the domain-generality of metacognition.