Paired corticomotoneuronal stimulation (or electrical PCMS: ePCMS) is the repetitive pairing of an electrical stimulus to a nerve with a transcranial magnetic stimulation of the primary motor cortex (TMS-of-M1) to noninvasively influence spinal plasticity. We compared ePCMS with the new painless PCMS protocol pairing a magnetic stimulus to the nerve with TMS-of-M1 (mPCMS) in the preactivated tibial anterior muscle (TA). Sixteen healthy adults participated in two sessions (mPCMS, ePCMS), each with 180 pairs of [low-intensity TMS-of-M1 + nerve stimulation] at 0.2 Hz. TA motor-evoked potentials (MEP) to single-pulse TMS at pre-PCMS, immediately and 30 min after PCMS, were cluster-analyzed to discriminate responders and non-responders. Paired-pulse TMS-of-M1 and F-waves were also tested and BDNF polymorphism influence was explored. Both PCMS protocols significantly increased MEP amplitudes (n = 9 responders each), but the time-course differed with mPCMS inducing larger MEP increase over time. The number of BDNF-methionine carriers tended to be larger than Val66Val in mPCMS and the reverse in ePCMS, thus warranting further investigations. The MEP changes of the preactivated TA likely occurred at the pre-motoneuronal level and larger mPCMS after-effects over time may be related to the afferents recruited. mPCMS seems relevant to be tested in future studies as a painless noninvasive approach to induce sustained pre-motoneuronal plasticity in spinal cord injury.