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Description: Literacy and numeracy are fundamental skills acquired in childhood, a time that coincides with considerable shifts in large-scale brain organisation. However, most studies emphasize focal brain contributions to literacy and numeracy development by employing case-control designs and voxel-by-voxel statistical comparisons. This approach has been valuable, but does not capture the potential importance of broader differences in brain organisation. The current study aims to address this by including children with varying levels of reading and maths ability, and by using a whole-brain structural connectome approach based on diffusion-weighted MRI data. Our results indicate an association between literacy and numeracy development and a distributed network of white matter connections that extends well beyond regions implicated in voxel-wise studies. Graph theory measures of network organisation were predictive of reading and maths scores. Simulated disruption of highly-connected hubs indicated that these regions are particularly important for optimal network organisation. These findings show that changes in large-scale brain organisation contribute to improvements in literacy and numeracy as children grow up.