It is well known that monosynaptic spinal reflexes and motor evoked potentials following transcranial magnetic stimulation (TMS) are reinforced during phasic and intensive voluntary contraction in the remote segment (remote effect). However, the remote effect on the cortical silent period (CSP) is less known. The purpose of the present study is to determine to what extent the CSP in the intrinsic hand muscle following TMS is modified by voluntary ankle dorsiflexion and to elucidate the origin of the modulation of CSP by the remote effect. CSP was recorded in the right first dorsal interosseous while subjects performed phasic dorsiflexion in the ipsilateral side under self-paced and reaction-time conditions. Modulation of the peripherally-induced silent period (PSP) induced by electrical stimulation of the ulnar nerve was also investigated under the same conditions. In addition, modulation of the CSP was investigated during ischemic nerve block of the lower limb and during application of vibration to the tibialis anterior tendon. The duration of CSP was significantly shortened by phasic dorsiflexion, and the extent of shortening was proportional to dorsiflexion force. Shortening of the CSP duration was also observed during tonic dorsiflexion. In contrast, the PSP duration following ulnar nerve stimulation was not altered during phasic dorsiflexion. Furthermore, the remote effect on the CSP duration was seen during ischemic nerve block of the lower limb and the pre-movement period in the reaction-time paradigm, but shortening of the CSP was not observed during tendon vibration. These findings suggest that phasic muscle contraction in the remote segment results in a decrease in intracortical inhibitory pathways to the corticospinal tract innervating the muscle involved in reflex testing and that the remote effect on the CSP is predominantly cortical in origin.