Motor training results in encoding of motor memories, a form of use-dependent plasticity. Here we tested the hypothesis that transcranial magnetic stimulation (TMS) synchronously applied to a motor cortex engaged in a motor training task could enhance this plastic process. Healthy volunteers were studied in four sessions: training consisting of performance of directionally specific voluntary thumb movements (Train alone), training with TMS delivered during the execution of the training movement in a strictly temporal relationship to the motor cortex contralateral (Train+TMS synchronous(contra)) and ipsilateral (Train+TMS synchronous(ipsi)) to the training hand, and training with TMS delivered asynchronous to the training movement to the motor cortex contralateral to the training hand (Train+TMS asynchronous(contra)). Train alone, Train+TMS synchronous(contra), and Train+TMS asynchronous(contra) but not Train+TMS synchronous(ipsi) elicited a clear motor memory. The longevity of the encoded memory was significantly enhanced by Train+TMS synchronous(contra) when compared with Train alone and Train+TMS asynchronous(contra). Therefore use-dependent encoding of a motor memory can be enhanced by synchronous Hebbian stimulation of the motor cortex that drives the training task and reduced by stimulation of the homologous ipsilateral motor cortex, a result relevant for studies of cognitive and physical rehabilitation.