Pharmaceutical compositions and methods for the treatment of Gulf War Illness in human patients comprising administering a central nervous system (CNS) stimulant in a daily low-dosage amount, and micronutrients acetyl L-carnitine, L-tyrosine, N-acetyl cysteine, and alpha-lipoic acid. The CNS stimulant and micronutrient components may be in admixture for convenient daily oral administration of a low dosage CNS stimulant and micronutrients in the range of about 60-250 mg acetyl L-carnitine, 50-200 mg L-tyrosine, 60-250 mg N-acetyl cysteine, and 25-100 mg alpha-lipoic acid per day.