Connections between the cerebellum and the contralateral motor cortex are dense and important, but their physiological significance is difficult to measure in humans. We have studied a group of 10 healthy subjects to test whether a modulation of the excitability of the left cerebellum can affect the excitability of the contralateral motor cortex. We used repetitive transcranial magnetic stimulation (rTMS) at 1 Hz frequency to transiently depress the excitability of the left cerebellar cortex and paired-pulse TMS testing of intracortical inhibition (ICI) and intracortical facilitation (ICF) to probe the excitability of cortico-cortical connections in the right motor cortex. The cortical silent period was also measured before and after cerebellar rTMS. Motor evoked potentials (MEPs) were significantly larger after than before conditioning rTMS trains (p < 0.01). Moreover, left cerebellar rTMS increased the ICF of the right motor cortex as measured with paired-pulses separated by an interstimulus interval (ISI) of 15 ms. The effect lasted for up to 30 min afterward and was specific for the contralateral (right) motor cortex. The cortical silent period was unaffected by cerebellar rTMS. The implication is that rTMS of the cerebellar cortex can shape the flowing of inhibition from Purkinje cells toward deep nuclei, thereby increasing the excitability of interconnected brain areas.