Objective: There seems to be no consensus in the literature regarding the protocol of surface electromyography (sEMG) electrode placement for recording motor evoked potentials (MEP) in transcranial magnetic stimulation (TMS) applications. Thus, the aim of this study was to investigate the effect on the MEP amplitude by two different protocols for electrode placement. Methods: SEMG electrodes were placed on three upper arm muscles (biceps brachii, flexor carpi radialis, and flexor pollicis brevis) of six right-handed subjects following two different protocols (1 and 2), which varied according to the interelectrode distance and location relative to the muscle. TMS pulses were applied to the hotspot of biceps brachii, while sEMG was recorded from the two protocols and for each muscle simultaneously. Main Results: Greater MEP amplitudes were obtained for Protocol 1 compared to Protocol 2 (P < 0.05). Significance: Different electrode placement protocols may result in distinct MEP amplitudes, which should be taken into account when adjusting the intensity on single and repetitive TMS sessions.