Severe postnatal systemic infection is highly associated with persistent disturbances in brain development and neurobehavioral outcomes in survivors of preterm birth. However, the contribution of less severe but prolonged postnatal infection and inflammation to such disturbances is unclear. Further, the ability of modern imaging techniques to detect the underlying changes in cellular microstructure of the brain in these infants remains to be validated. We used high-field ex-vivo MRI, neurohistopathology, and behavioral tests in newborn rats to demonstrate that prolonged postnatal systemic inflammation causes subtle, persisting disturbances in brain development, with neurodevelopmental delays and mild motor impairments. Diffusion-tensor MRI and neurite orientation dispersion and density imaging (NODDI) revealed delayed maturation of neocortical and subcortical white matter microstructure. Analysis of pyramidal neurons showed that the cortical deficits involved impaired dendritic arborization and spine formation. Analysis of oligodendrocytes showed that the white matter deficits involved impaired oligodendrocyte maturation and axonal myelination. These findings indicate that prolonged postnatal inflammation, without severe infection, may critically contribute to the diffuse spectrum of brain pathology and subtle long-term disability in preterm infants, with a cellular mechanism involving oligodendrocyte and neuronal dysmaturation. NODDI may be useful for clinical detection of these microstructural deficits.