56Fe-particle radiation-induced brain disturbances are a major health concern for astronauts during long-term space travel. The present study investigated temporal modifications within the brain after 56Fe-particle exposure using in vivo magnetic resonance imaging (MRI) correlated to histology. Male Sprague-Dawley rats were exposed to brain-only 56Fe-particle radiation. MRI including T2-weighted, diffusion-weighted, pre/postcontrast enhanced T1-weighted imaging was performed 0.25–18 months after exposure. T2 relaxation times and the apparent diffusion coefficient were quantified within the hippocampus, entorhinal cortex, retrosplenial cortex and thalamus, and correlative histopathology was then performed at each time. In the absence of visible lesions on MR images, the apparent diffusion coefficient and T2 relaxation times revealed 56Fe-particle-induced dynamic changes in all ROIs over the 18-month time course. The patterns of MR changes were spatially similar within the different regions. The temporal alterations in the apparent diffusion coefficient corresponded to the glial cell changes within the brain. Quantitative MRI provides a non-invasive approach to monitor spatio-temporal brain alterations after 56Fe-particle irradiation. The apparent diffusion coefficient appears to be a sensitive metric to reveal ongoing tissue modifications involving multiple cellular components in vivo.