A neural synchrony model of cognitive control is proposed. It construes cognitive control as a higher-level action to synchronize lower-level brain areas. Here, a controller prefrontal area (medial frontal cortex) can synchronize two cortical processing areas. The synchrony is achieved by a random theta frequency-locked neural burst sent to both areas. The choice of areas that receive this burst is determined by lateral frontal cortex. As a result of this synchrony, communication between the two areas becomes more efficient. The model is tested on the classical Stroop cognitive control task, and its operation is explored in several simulations. Both reactive and proactive controls are implemented via theta power modulation. Increasing theta power improves behavioral performance; furthermore, via theta–gamma phase–amplitude coupling, theta also increases gamma frequency power and synchrony in posterior processing areas. Thus, the model solves a central computational problem for cognitive control (how to allow rapid communication between arbitrary brain areas), while making rich contact with behavioral and neurophysiological data.