The present study aimed to quantitatively characterize changes in the whole brain and arterial morphology in response to prenatal ionizing irradiation. Magnetic resonance imaging (MRI) and angiography (MRA) were used to evaluate brain and arterial abnormalities in 8‐week‐old male mice prenatally exposed to X‐ray radiation at a dose of 0.5 or 1.0 Gy on embryonic day (E) 13. Irradiated mice demonstrated decreased brain volume, increased ventricular volume, and arterial malformation. Additionally, MRA signal intensity and arterial thickness in the anterior cerebral artery, middle cerebral artery, and basilar artery were lower in radiation‐exposed mice than in control mice. MRI and MRA are useful tools for assessing brain and arterial abnormalities after prenatal exposure to radiation.