In this review, begin with a brief review of functional connectivity and network theory. We then explore how neuroimaging and neurophysiology are being used to study functional connectivity networks, and provide insight into the distributed nature of common brain diseases. Next, we review basic principles of noninvasive brain stimulation techniques and the evidence that these techniques have network effects beyond the stimulation site. Finally, we provide examples of how these tools can be combined to understand, and selectively manipulate functional connectivity networks. We focus on three clinical conditions (stroke, depression, and schizophrenia) to illustrate how abnormal network dynamics may underlie common brain diseases, and how manipulation of these networks through noninvasive brain stimulation represents a promising therapeutic intervention.