Introduction While repetitive transcranial magnetic stimulation (rTMS) is a promising alternative in treatment resistant depression (TRD) the optimal coil placement and stimulation protocol, as well as its mechanism of action, are still largely unknown. Methods Here, 20 patients with major depressive disorder (MDD) were randomized to two weeks of two daily sessions of active or sham intermittent theta burst stimulation (iTBS). The iTBS was applied with 90% of resting foot motor threshold, 1200 pulses/session, two seconds stimulation and eight seconds pause. Stimulation was applied over the dorsomedial prefrontal cortex (dmPFC) using neuronavigation and an angled coil for deeper stimulation [1] . Resting-state functional magnetic resonance imaging was performed one day before treatment onset and again four weeks later. A spherical seed was defined around the target coordinate for treatment within dorsal anterior cingulate cortex (dACC) to assess whole brain functional connectivity. Results An interaction between treatment condition (sham vs. active) and time (before vs. after iTBS) was observed in the posterior hippocampus, thalamus and calcarine sulcus within the left hemisphere, reflecting increased connectivity in the active treatment group only. Conclusion The findings suggest that stimulation of the dmPFC and underlying dACC modulates its connectivity with distal subcortical structures and may be an underlying treatment mechanism of iTBS in MDD.