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Repetitive peripheral magnetic stimulation (rPMS) can improve motor dysfunction and spasticity in individuals with central nervous system lesions. However, its underlying neural mechanisms remain poorly understood. This study investigated the effects of 15-min rPMS applied to the wrist extensor muscles on reciprocal inhibition between the wrist flexor and extensor muscles in healthy adults. First, to assess distinct inhibitory mechanisms, the effects of rPMS on reciprocal inhibition directed from extensor carpi radialis (ECR) to the flexor carpi radialis (FCR) were examined using the FCR H-reflex conditioned by radial nerve stimulation by assessing disynaptic Ia inhibition and D1 inhibition at conditioning–test intervals of −0.3 ± 0.2 ms and 13 ms, respectively. At an intensity sufficient to elicit muscle contraction, rPMS significantly enhanced disynaptic Ia inhibition, but had no significant effect on D1 inhibition. Next, we assessed the effects of rPMS on disynaptic Ia inhibition and D1 inhibition directed in the opposite direction from FCR to ECR. In this case, rPMS significantly reduced disynaptic Ia inhibition but had no significant effect on D1 inhibition. Furthermore, rPMS did not alter the excitability of monosynaptic reflex pathways in the stimulated ECR or its antagonist FCR. Taken together, these findings indicate that rPMS applied to the wrist extensor muscles enhances disynaptic Ia inhibition from the stimulated muscles to their antagonist motoneurons and attenuates disynaptic Ia inhibition in the opposite direction, suggesting that rPMS modulates disynaptic Ia inhibition in a direction-dependent manner.