Introduction: Excitotoxicity plays an important role in the pathogenesis of the preferential motor neuron death observed in amyotrophic lateral sclerosis (ALS). Continuous theta burst stimulation (cTBS) by transcranial magnetic stimulation has an inhibitory effect on corticospinal excitability (CSE). We characterized the neurophysiological changes induced by cTBS in ALS. Methods: The patients received 5 daily sessions of cTBS. CSE was assessed at baseline and after each session of cTBS. Results: The amplitude of a single pulse motor evoked potential was significantly decreased (34%) over the days. The amplitude returned to baseline a week after the last session. The resting motor threshold increased significantly, whereas intracortical inhibition and facilitation did not change over the sessions. Conclusions: Daily cTBS has a cumulative depressing effect on CSE in patients with ALS. These results suggest that modulation of CSE in ALS is possible, but repetitive sessions are needed to maintain the effect. © 2013 Wiley Periodicals, Inc.