A stranded male harbor seal (Phoca vitulina) neonate with progressive clinical signs of ataxia, tremors, and deteriorating consciousness was evaluated using magnetic resonance imaging for suspected cerebellar brain disease prior to euthanasia because of grave prognosis. Magnetic resonance imaging identified occipital bone dysplasia with cerebellar herniation and concurrent atlantoaxial subluxation with spinal cord compression. These imaging findings elucidated the cause of histopathology changes including gliosis of the cerebellum and axonal degeneration and dilation of myelin sheaths of the dorsal funiculus of the spinal cord. Occipital bone dysplasia and/or atlantoaxial subluxation should be considered as differentials for abnormal neurologic signs in harbor seal neonates. Magnetic resonance imaging is a valuable modality for antemortem diagnosis.