Microstructural development is dynamic throughout childhood and adolescence. Modelling these profiles requires statistical flexibility to understand complex interplays between related phenotypes such as sex, pubertal stage, and age. We leverage the fixel-based analysis framework and compute fibre density and morphology metrics in selective white matter tracts, to enable longitudinal mixed-effects modelling of multiple phenotypes. We show that longitudinal development of white matter fibre properties in children aged 9–14 dominates in posterior fibres. Increases in fibre density are associated with increases in pubertal stage and attention dysfunction, and protracted increases in fibre density are associated with greater internalising behaviours.