Pre-reading language skills develop rapidly in early childhood and are related to brain structure and function in young children prior to formal education. However, the early neurobiological development that support these skills is not well understood and has not been assessed longitudinally using multiple imaging approaches. Here we acquired anatomical, diffusion tensor imaging (DTI) and resting state functional MRI (rs-fMRI) from 35 children at 3.5 years of age. Children were assessed for pre-reading abilities using the NEPSY-II subtests one year later (4.5 years). We applied a data-driven linked independent component analysis to explore the shared co-variation of grey and white matter measures. Two sources of structural variation at 3.5 years of age demonstrated a weak relationship with Speeded Naming scores at 4.5 years of age. The first imaging component involved volumetric variability in reading-related cortical regions alongside microstructural features of the superior longitudinal fasciculus. The second component was dominated by cortical volumetric variations within the cerebellum and visual association area. In a subset of children with rs-fMRI data, we evaluated the inter-network functional connectivity of the left-lateralized fronto-parietal language (FPL) network and its relationship with pre-reading measures. Higher functional connectivity between the FPL functional network and the default mode and visual networks at 3.5 years predicted better Phonological Processing scores at 4.5 years. Together, these results suggest that the integration of functional networks, as well as the co-development of white and grey matter brain structures in early childhood, may support the emergence of pre-reading measures in preschool children.