Transcranial direct current stimulation (tDCS) is a noninvasive brain stimulation technique that modulates the cortical excitability of the human brain by applying weak direct currents on the scalp through both anodal and cathodal electrodes. However, the mechanisms of tDCS action are not yet fully understood. Therefore, researchers are trying to figure out the mechanisms of tDCS effect with the modulation of functional connectivity by combining tDCS and brain imaging techniques. In this chapter, we provide an overview of the effects of motor cortex and prefrontal tDCS on functional MRI connectivity in healthy subjects and patients with psychiatric and neurological disorders using both resting-state and task-based fMRI paradigms. Furthermore, we also discuss variability, test-retest reliability of tDCS, and possible MRI markers of clinical response to individually predict the therapeutic effects of prefrontal tDCS.