Herein, we present a case of heatstroke encephalopathy with abnormal brain magnetic resonance imaging (MRI) signals. A 19-year-old man lost consciousness while working outdoors when the temperature was 35°C. His Glasgow Coma Scale score at presentation was E1V1M1, and his body temperature was 39°C. Chest computed tomography revealed bilateral infiltrates, and tests for urinary pneumococcal antigens were positive. He was diagnosed with heatstroke preceded by pneumococcal pneumonia. He was subsequently treated with antibiotics, and body surface cooling was performed. A diffusion-weighted brain MRI performed on day eight revealed abnormal bilateral hyperintensities from the cortex at the frontal lobe apex of the subcortex. Moreover, he had reduced spontaneity, dysarthria, nystagmus, tremor, and ataxia of both the upper limbs. He was diagnosed with heatstroke encephalopathy. On day 28 since admission, the abnormal MRI signals disappeared. Subsequently, the patient’s spontaneity improved, but his other neurological dysfunctions persisted. This case study demonstrates that MRI may not be a sensitive indicator of the prognosis of heatstroke encephalopathy.