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Introduction. Mild cognitive impairment (MCI) negatively affects patients quality of life and is a risk factor for dementia. One of the main causes of MCI is cerebral small vessel disease (CSVD). The previously established link between decreased activity in the supplementary motor area (SMA) and cognitive impairment in patients with CSVD makes it possible to consider repetitive transcranial magnetic stimulation (rTMS) of the SMA with functional magnetic resonance imaging (fMRI)-assisted positioning as a promising method for treating MCI caused by CSVD. The aim of the study was to evaluate the efficacy and tolerability of fMRI-guided rTMS of the SMA in patients with MCI caused by CSVD. Materials and methods. Twenty patients were randomly assigned to the intervention (SMA stimulation; n = 10) and the control (vertex stimulation; n = 10) groups. All patients underwent 10 sessions of high-frequency rTMS. The MoCA scale, trail making test, Tower of London test, and copying and delayed recall in the ReyOsterrieth complex figure test were used to assess treatment effect. Testing was conducted before, immediately after and 3 months post rTMS. Results. The intervention group demonstrated a significant improvement in the MoCA, the Tower of London test and delayed recall in the ReyOsterrieth complex figure test immediately after rTMS. Statistically significant improvement in the MoCA and the Tower of London test results was maintained after 3 months. No statistically significant improvements were found in the control group. Groups were comparable in the incidence of headache during and in the 24-hour period after the stimulation session, and in unpleasant sensations during the session. Conclusion. fMRI-guided rTMS of the SMA is an effective and promising treatment method for MCI caused by CSVD, with effects lasting three or more months, and good tolerability.