The present invention relates to a pharmaceutical composition for protecting neurons or for preventing and treating ischemic neuronal diseases comprising the extract of Lithospermum erythrorhizon Sieb. Et Zucc extracted with water, low-alcohols or their mixture or acetylshikonin separated therefrom as an effective ingredient. The extract of Lithospermum erythrorhizon Sieb. Et. Zucc or acetylshikonin separated therefrom of the present invention has neuronal protective effect, so that it not only interrupts the development of ischemic neuronal diseases but also is very safe, indicating that the extract or acetylshikonin can be used as a medicinal drug for prevention and treatment of degenerative brain disease caused by neuronal apoptosis such as stroke, apoplexy, dementia, Alzheimer's disease, Parkinson's disease, Huntington's disease, Pick's disease and Creutzfeldt-Jakob disease and further can be developed as functional health food.