Theta-burst stimulation (TBS) is widely used due to induction of the long-lasting effects with short protocol duration. To reduce the variability of the effect, approaches to personalize it, such as using theta-gamma coupling frequencies (TGC), are being investigated. The study was aimed to develop the personalized protocol of navigated intermittent theta-burst stimulation (iTBS-ind) based on TGC, and to compare this protocol with the standard one (iTBS-5/50) and sham stimulation (iTBS-sham). The study involved 16 healthy volunteers (М — 7; 29.6 years), who were randomized to receive one session of each protocol of the left dorsolateral prefrontal cortex iTBS. The effects were estimated using the n-back test with simultaneous presentation of verbal and spatial stimuli (n = 2, 3), Digit Span test, Corsi blocks task, Tower of London test; testing was performed immediately before, immediately after and 60 min after stimulation. No severe adverse events were reported. Significant effect was obtained when performing assessment after 60 min for iTBS-5/50 in the n-back test with spatial stimuli (n = 3) (p_corr = 0.018), for all protocols in the Tower of London test (p_corr = 0.039 for iTBS-5/50, p_corr = 0.045 for iTBS-ind, p_corr = 0.003 for iTBS-sham). The iTBS-5/50 effect was significantly higher compared to iTBS-sham in the spatial n-back test (n = 3) (p_corr = 0.039), but lower compared to iTBS-ind and iTBS-sham in the Corsi blocks task (p_corr = 0.038 and 0.048, respectively). Thus, we failed to confirm the personalized protocol efficacy and superiority to the standard protocol and sham stimulation. Considering the effect of standard protocol, its further investigation can be promising.