The primary motor cortex (M1) plays a critical role in early aspects of motor skill learning. Given the notion of inter-hemispheric competition, unilateral disruption of M1 may increase excitability of the unaffected motor cortex and thus improve motor learning with the ipsilateral hand. We applied slow-frequency repetitive transcranial magnetic stimulation (rTMS) before the initiation of practice of a simple motor skill. Participants were randomly divided into three stimulation groups: (i) ipsilateral M1; (ii) contralateral M1; and (iii) Cz (control site). The mean execution time and error rate were recorded in four sessions distributed over 2 days. Disruption of M1 with rTMS slowed down skill acquisition with the contralateral hand, albeit non significantly, but paradoxically enhanced learning with the ipsilateral hand. This was evidenced by a significant decrease of execution time at the end of day 1 in the group that received rTMS over the ipsilateral M1 compared with both control groups (Cz and contralateral M1 stimulation). This supports the notion of inter-hemispheric competition and provides novel insights that may be applicable to neurorehabilitation.