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Background: The aim of this work was to investigate the efficacy of Transcranial Magnetic Therapy (TMT) on Fatigue in Multiple Sclerosis patients. It was conducted in outpatient clinic in Faculty of Physical Therapy, Cairo University. Subjects and Methods: Thirty Multiple Sclerosis patients from both sexes.The patient's age ranged from twenty to forty years. They were assigned randomly into two equal groups; the study group (GA) and the control group B (GB).The assessment of fatigue is done before and after treatment for both groups by Fatigue Severity Scale(FSS) and Fatigue Assessment Scale(FAS). Assessment of Multiple Sclerosis symptoms was done before and after treatment for both groups by Expanded Disability Status Scale(EDSS). Study group treated by TMT (Low intensity and low frequency) in addition to a selected physical therapy program for fatigue(Treadmail training, bicycle training and deep diaghragmatic breathing exercises). Control group treated by the same program of treatment as the GB without TMS. The duration of treatment was six weeks. Conclusion:application of TMT with low intensity and low frequency had a positive effect in decreasing MS fatigue.