In this paper we investigated the effects of intermittent theta-burst stimulation (iTBS) applied to the primary motor cortex on practice-related changes in motor performance. Seventeen healthy subjects underwent two experimental sessions, one testing real iTBS and the other testing sham iTBS. Before and after both iTBS sessions, the subjects practiced fast right index-finger abductions for a few minutes. As measures of cortical excitability we calculated resting motor threshold and motor-evoked potential amplitude. As measures of practice-related changes we evaluated the mean movement amplitude, peak velocity and peak acceleration values for each block. When subjects practiced the movement task, the three variables measuring practice-related changes improved to a similar extent during real and sham iTBS whereas cortical excitability increased only during real iTBS. In a further group of five healthy subjects we investigated the effect of real and sham iTBS on changes in motor performance after a longer task practice and found no significant changes in motor performance and retention after real and sham iTBS. From our results overall we conclude that in healthy subjects iTBS applied to the primary motor cortex leaves practice-related changes in an index finger abduction task unaffected. We suggest that iTBS delivered over the primary motor cortex is insufficient to alter motor performance because early motor learning probably engages a wide cortical and subcortical network.