Abstract A rapid plantar flexion perturbation in the early stance phase of walking elicits a large stretch reflex in tibialis anterior (TA). In this study we use repetitive Transcranial Magnetic Stimulation (rTMS) to test if this response is mediated through a transcortical pathway. TA stretch reflexes were elicited in the early stance phase of the step cycle during treadmill walking. 20 minutes of 1 Hz rTMS at 115% resting motor threshold (MTr) significantly decreased (p<0.05) the magnitude of the later component of the reflex at a latency of ~100 ms up to 25 min after the rTMS. Control experiments in which stretch reflexes were elicited during sitting showed no effect on the spinal mediated short and medium latency stretch reflex (SLR and MLR) while the long-latency stretch reflex (LLR) and the motor evoked potential (MEP) showed a significant decrease 10 minutes after 115% MTr rTMS. This study demonstrates that 1 Hz rTMS applied to the leg area of the motor cortex can suppress the long latency TA stretch reflex during sitting and in the stance phase of walking. These results are in line with the hypothesis that the later component of the TA stretch reflex in the stance phase of walking is mediated by a transcortical pathway. An alternative explanation for the observed results is that the reflex is mediated by subcortical structures that are affected by the rTMS. This study also shows that rTMS may be used to study neural control of walking.