The effect of accelerated intermittent theta burst stimulation (aiTBS) is investigated in three resting-state networks involved in depression: default mode network (DMN), central executive network (CEN), and salience network (SN). Multivariate Granger causality analysis was performed between time-series representing each network and between time-series of nodes belonging to these networks. The effects of the latter analysis were quantified by the in- and out-degree. No between-network effects were found but specific connections showed increased or decreased Granger causality after stimulation. Clinical responders showed changes in the in- and out-degree of the anterior cingulate, known to be important in depression pathology.