<p><b>Objectives.</b> To compare the clinical outcome and tolerability of transcranial magnetic stimulation (rTMS) using different stimulation protocols and to determine the dynamics of neurophysiological indexes of the functional state of the brain. <b>Materials and methods.</b> The study included 28 patients (mean age 23.5 ± 4.4 years) diagnosed with psychometrically confirmed F21 or F31–F34 and clinically significant depression (mean score on the Hamilton Depression Rating Scale (HDRS) 21.7 ± 5.6). Treatment included combined medication and rTMS of the left dorsolateral prefrontal cortex using two different protocols: 10 Hz (<i>n</i> = 16) and intermittent θ-burst stimulation (<i>n</i> = 12), which were randomly assigned. EEG recordings were made in all patients, both EEG and fMRI were made in patients undergoing θ-burst stimulation. The treatment efficacy criterion was a ≥25% reduction in the psychometric assessment; responders were identified when reductions were by ≥50%. <b>Results.</b> A total of 64.9% of patients were found to respond to the treatment; similarities in the frequency of clinical outcomes on use of different rTMS protocols were also noted. EEG results pointed to different neurophysiological mechanisms underlying changes in the state of the brain during treatment using different transcranial magnetic stimulation protocols. <b>Conclusion</b>s<b>.</b> Thus, a pilot study of the use of two rTMS protocols (without direct comparison) demonstrated definite efficacy in the treatment of depressive disorders in young male patients. Analysis of neurophysiological data led to the cautious suggestion that high-frequency stimulation at a frequency of 10 Hz (associated with a decrease in the θ activity index, which may be due to the “normalization” of limbic-cortical interactions) and intermittent stimulation with θ bursts (associated with the “normalization” of altered interhemispheric asymmetry) have different mechanisms of action.</p>