Repetitive transcranial magnetic stimulation (rTMS) modulates cortical excitability beyond the duration of the rTMS trains themselves. Depending on rTMS parameters, a lasting inhibition or facilitation of cortical excitability can be induced. Therefore, rTMS of high or low frequency over motor cortex may change certain aspects of motor learning performance and cortical activation. This study investigated the effect of high and low frequency subthreshold rTMS applied to the motor cortex on motor learning of sequential finger movements and brain activation using functional MRI (fMRI). Three healthy right-handed subjects (mean age 23.3) were enrolled. All subjects were trained with sequences of seven-digit rapid sequential finger movements, 30 minutes per day for 5 consecutive days using their left hand. 10 Hz (high frequency) and 1 Hz (low frequency) trains of rTMS with 80% of resting motor threshold and sham stimulation were applied for each subject during the period of motor learning. rTMS was delivered on the scalp over the right primary motor cortex using a figure-eight shaped coil and a Rapid(R) stimulator with two Booster Modules (Magstim Co. Ltd, UK). Functional MRI (fMRI) was performed on a 3T ISOL Forte scanner before and after training in all subjects (35 slices per one brain volume TR/TE = 3000/30 ms, Flip angle , FOV 220 mm, matrix, slice thickness 4 mm). Response time (RT) and target scores (TS) of sequential finger movements were monitored during the training period and fMRl scanning. All subjects showed decreased RT and increased TS which reflecting learning effects over the training session. The subject who received high frequency rTMS showed better performance in TS and RT than those of the subjects with low frequency or sham stimulation of rTMS. In fMRI, the subject who received high frequency rTMS showed increased activation of primary motor cortex, premotor, and medial cerebellar areas after the motor sequence learning after the training, but the subject with low frequency rTMS showed decreased activation in above areas. High frequency subthreshold rTMS on the motor cortex may facilitate the excitability of motor cortex and improve the performance of motor sequence learning in normal subject.