Cognitive neuroscience offers a series of tools and methodologies that allow researchers in the field of learning and instruction to complement and extend the knowledge they have accumulated through decades of behavioral research. The appropriateness of these methods depends on the research question at hand. Cognitive neuroscience methods allow researchers to investigate specific cognitive processes in a very detailed way, a goal in some but not all fields of the learning sciences. This value added will be illustrated in three ways, with examples in field of mathematics learning. Firstly, cognitive neuroscience methods allow one to understand learning at the biological level. Secondly, these methods can help to measure processes that are difficult to access by means of behavioral techniques. Finally, and more indirectly, neuroimaging data can be used as an input for research on learning and instruction. This paper concludes with highlighting the challenges of applying neuroscience methods to research on learning and instruction.