Flexible interaction between brain regions enables neural systems to transfer and process information adaptively for goal-directed behaviors. In the current study, we investigated neural substrates that interact with task-evoked functional connectivity during cognitive control. We conducted a human fMRI study where participants selectively attended to a category of visual stimuli in the presence of competing distractors from another stimulus category. To study flexible interactions between brain regions, we performed a dynamic functional connectivity analysis to estimate temporal changes in connectivity strength between brain regions under different levels of cognitive control. Consistent with theoretical predictions, we found that cognitive control selectively enhances functional connectivity for prioritizing the processing of task-relevant information. By regressing temporal changes in connectivity strength against activity patterns elsewhere in the brain, we localized frontal and parietal regions that potentially provide top-down biasing signals for influencing, or reading information out from, task-evoked functional connectivity. Our results suggest that in addition to modulating local activity, frontoparietal regions could also exert top-down biasing signals to influence functional connectivity between distributed brain regions.