Pediatric cranial radiation therapy can induce long-term neurocognitive deficits, the risk and severity of these deficits are amplified in females and in those individuals exposed at a younger age and/or those irradiated at higher doses. To investigate the developmental consequences of these factors in greater detail, male and female C57Bl/6J mice between infancy and late childhood (16 and 36 days) were irradiated at a single time point with a whole-brain dose of 0, 3, 5 or 7 Gy. In vivo and ex vivo magnetic resonance imaging (MRI) and deformation-based morphometry was used to identify radiation-induced volume differences. As expected, exposure to 7 Gy of radiation at 16 days of age induced widespread volume deficits that were largely mitigated by increasing treatment age or decreasing dose. Notable exceptions were regions in the olfactory bulbs and hippocampus that displayed both a detectable difference in volume and a loss in neurogenesis for most doses and ages. Furthermore, white matter regions located at the front of the brain remained sensitive to radiation at later treatment ages, compared to regions at the back. Differences due to sex were subtle, with increased radiosensitivity in females detectable only in the mammillary bodies and fornix. Our results reveal anatomical alterations in brain development consistent with expectations based on pediatric patient neurocognitive outcomes. This data demonstrates that neuroimaging of the mouse is an effective tool for investigating radiation-induced late effects.