While it is often reported that musical experience can have positive effects on cognitive development in young children, the neural basis of such potential effects remains relatively unexplored. Employing functional magnetic resonance imaging (fMRI) for such research presents as many challenges as possibilities, not least of which is the fact that young children can find it difficult to remain still and attentive for long periods of time. Here we describe an fMRI scanning protocol designed specifically for young children using short scanning runs, a sparse temporal sampling data acquisition technique, simple rhythmic and melodic discrimination tasks with a button-press response, and a child-oriented preparation session. Children were recruited as part of a large-scale longitudinal study examining the effects of musical training on cognitive development and the structure and function of the growing brain. Results from an initial analysis of 33 children and from the first five children to be re-scanned after musical training indicate that our scanning protocol is successful and that activation differences can be detected both between conditions and over time.