Stanford neuromodulation therapy (SNT) is the state-of-the-art magnetic stimulation protocol that has been developed for management of treatment-resistant depression (TRD). The study was aimed to assess the possibility of SNT implementation in clinical practice and to define the protocol safety and efficacy in patients with TRD being an episode of the recurrent depressive disorder or bipolar disorder at the independent center. The study involved six patients (among them three women aged 21–66) with TRD associated with recurrent depression and type 1 or 2 bipolar disorder. The patients received intermittent theta-burst stimulation in accordance with the SNT protocol for five days: applying 10 triple blocks of stimulation daily at intervals of 1 hr between the blocks to the selected stimulation site showing maximum negative functional connectivity with subgenual cingulate cortex within the left dorsolateral prefrontal cortex. The Montgomery–Asberg Depression Rating Scale (MADRS) was used for clinical assessment of the effects, the follow-up period was three months. The improvement of depressive symptoms to the levels characteristic of remission immediately after the SNT completion was observed in five patients (MADRS score ≤10). After three months, two patients still had remission, the condition of three patients met the criteria of mild depressive episode, and one female patient withdrew from the study due to logistical difficulties. No serious adverse events were reported. The findings confirm safety and potentially high efficacy of SNT, including in patients with type 1 and 2 bipolar disorders.