Dynamic networking of brain regions is suggested to be one of the key factors involved in various brain computations. Central executive function typically requires instantaneous coordination among the medial prefrontal regions and other distant regions, depending on the on-going task situation. In human scalp-recorded electroencephalography (EEG), the medial prefrontal area is estimated to be the current source of the theta rhythm, while there is no direct evidence that the theta rhythm is involved in the dynamic networking of central executive circuits. Here we hypothesize that the central executive circuit over the prefrontal and task-related cortices is dynamically linked by theta synchronization. By using simultaneous functional magnetic resonance imaging (fMRI) and EEG, we elucidated cortical circuits emerging with theta phase synchronization during free pacing repeated subtraction. Theta phase synchronization in the scalp EEG was found to emerge at two major clusters of electrode pairs, between the right frontal and left parietal sites and between the frontal and right parietal sites. The phase synchronization of two clusters is accompanied by fMRI responses in the cortical regions responsible for central executive function, working memory, visual imagery and cognitive action sequence. Here we report the first evidence that theta phase synchronization dynamically coordinates the central executive circuits, including the medial prefrontal cortex and relevant cortical regions.