Objective: Quadripulse magnetic stimulation (QPS) is useful for changing corticospinal excitability, but the long-term depression (LTD)-like effect considerably has low responder rate. To solve this problem, we modified inhibitory QPS (QPSLTD) by pairing it with the application of an electrical stimulus (ES) to peripheral nerves (paired-associative QPS [PA-QPSLTD]), and investigated the effects of PA-QPSLTD on motor-evoked potentials (MEPs). Methods: The peripheral-nerve ES was applied at two timings with a synchrony to transcranial magnetic stimulation (TMS) over the primary motor cortex (M1). The intrapair interval between ES and TMS was the N20-peak latency plus 2 ms for PALTP-QPSLTD, and N20-peak latency minus 5 ms for PALTD-QPSLTD. MEPs elicited by TMS over the left M1 were recorded from the right abductor pollicis brevis muscle before and after the interventions. The responder rates of PALTD-QPSLTD and QPSLTD was also studied. Results: The PALTD-QPSLTD induced larger LTD-like effect than QPSLTD, and the PALTP-QPSLTD induced smaller aftereffect than QPSLTD. The responder rates were significantly higher for PALTD-QPSLTD than for QPSLTD. Conclusions: The new protocol, PALTD-QPSLTD, induces powerful and consistent LTD-like aftereffects in the corticospinal tract neurons. Significance: PALTD-QPSLTD is suitable for use in physiological evaluations and therapeutic approaches in various neurological disorders. © 2022 International Federation of Clinical Neurophysiology