Navigated transcranial magnetic stimulation (nTMS) over the supplementary motor area (SMA) may impact fine motor skills. This study evaluates different nTMS parameters in their capacity to affect fine motor performance on the way to develop an SMA mapping protocol. Twenty healthy volunteers performed a variety of fine motor tests during baseline and nTMS to the SMA using 5 Hz, 10 Hz, and theta-burst stimulation (TBS). Effects on performance were measured by test completion times (TCTs), standard deviation of inter-tap interval (SDIT), and visible coordination problems (VCPs). The predominant stimulation effect was slowing of TCTs, i.e. a slowdown of test performances during stimulation. Furthermore, participants exhibited VCPs like accidental use of contralateral limbs or inability to coordinate movements. More instances of significant differences between baseline and stimulation occurred during stimulation of the right hemisphere compared to left-hemispheric stimulation. In conclusion, nTMS to the SMA could enable new approaches in neuroscience and enable structured mapping approaches. Specifically, this study supports interhemispheric differences in motor control as right-hemispheric stimulation resulted in clearer impairments. The application of our nTMS-based setup to assess the function of the SMA should be applied in patients with changed anatomo-functional representations as the next step, e.g. among patients with eloquent brain tumors.