A 47-year-old man presented to our hospital after suffering transient loss of consciousness and falling to the floor. On admission, his Glasgow Coma Scale score was 11 (E3V3M5), and he exhibited restlessness. Blood examination revealed hyperthyroidism. Computed tomography showed slight traumatic subarachnoid hemorrhage. He developed fever and tachycardia, and was diagnosed with thyroid crisis. Magnetic resonance imaging showed a brain contusion in the right frontal lobe, and encephalopathy signs in the right frontal and insular cortex. Immunocytochemical examinations suggested Hashimoto's disease, and hormone examinations revealed plasma levels were undetectably low of adrenocorticotropic hormone (ACTH) and low of cortisol. Pituitary stimulation tests showed inadequate plasma ACTH and cortisol response, consistent with isolated ACTH deficiency (IAD). The final diagnosis was IAD associated with Hashimoto's disease. Hydrocortisone replacement therapy was continued, and the patient was nearly free from neurological deficits after 18 months. The neuroimaging abnormalities gradually improved with time.