Tracing the connections from brain functions to children’s cognitive development and education is a major goal of modern neuroscience. We performed the first meta-analysis of functional magnetic resonance imaging (fMRI) data obtained over the past decade (1999–2008) on more than 800 children and adolescents in three core systems of cognitive development and school learning: numerical abilities, reading, and executive functions (i.e. cognitive control). We ran Activation Likelihood Estimation (ALE) meta-analyses to obtain regions of reliable activity across all the studies. The results indicate that, unlike results usually reported for adults, children primarily engage the frontal cortex when solving numerical tasks. With age, there may be a shift from reliance on the frontal cortex to reliance on the parietal cortex. In contrast, the frontal, temporo-parietal and occipito-temporal regions at work during reading in children are very similar to those reported in adults. The executive frontal regions are also consistent with the imaging literature on cognitive control in adults, but the developmental comparison between children and adolescents demonstrates a key role of the anterior insular cortex (AIC) with an additional right AIC involvement in adolescents.