Background Patients with incomplete spinal cord injuries (iSCI) present impairment of motor and sensory functions associated with increased spasticity. The repetitive transcranial magnetic stimulation (rTMS) becomes widely used to potentiate the effects of long-lasting physical rehabilitation in the iSCI subjects. The purpose of this study was ascertaining the early changes in activity of motor muscles units and spinal cord efferent transmission studied with surface electromyography (sEMG) and motor evoked potentials (MEPs) recordings after five repeated sessions of rTMS applied every month to the iSCI subjects along with rehabilitation. Material and methods Twenty-eight subjects with iSCI at C2-Th12 levels were subjected to twenty sessions of rTMS for five months (three to four sessions every month). Subjects received 800 biphasic pulses (20 Hz, 2s trains, 28s ITI, 36–38% MSO) per day bilaterally over the primary motor cortex areas (MagVenture). sEMG at rest and during attempts of maximal contraction lasting five seconds and MEPs recordings from five observation periods were analyzed before and after rTMS. Results After five rTMS meetings a significant decrease in sEMG amplitudes recorded at rest and increase of mean sEMG amplitudes recorded during maximal contraction were observed. A moderate increase of mean MEPs amplitudes was observed on certain observation period. Conclusions rTMS provided decrease of spasticity as evaluated in sEMG recordings at rest and evoked simultaneous improvement of muscle’s motor units’ contractions as well as the efferent transmission in spinal pathways in the iSCI subjects. The study was supported by the Nicholls Spinal Injury Foundation, UK .