Schizophrenia is associated with cognitive deficits affecting daily life. The dysconnectivity hypothesis of schizophrenia postulates that disrupted neural communication patterns are causal for the onset of various symptoms. In the present study we examined the functional connectivity in the electroencephalogram (EEG) between fronto-medial and fronto-lateral sites since prefrontal lobe areas are associated with executive functioning. The connectivity was quantified by the inter-site phase clustering (ISPC) representing the consistency of phase angles of two oscillatory processes. The ISPC was analyzed in the theta frequency range being related to cognitive control processes. 29 patients suffering from schizophrenia (SZP) and 29 matched healthy controls (HC) performed a Go/NoGo task while an EEG was recorded. SZP showed worse Go/NoGo performance (d’). Regarding the phase-based connectivity, the NoGo trials elicited a generally higher ISPC than the Go trials. A group difference was only detectible on at a descriptive level (HC>SZP), the interaction of condition and group was not significant. In separate analyses within groups, in SZP an increase of ISPC in the NoGo trials was positively associated with performance (d’), whereas in the HC group an increase of ISPC was negatively correlated with performance. Taken together, the differences in theta phase-based connectivity between fronto-medial and fronto-lateral sites may reflect the levels of conflict detection and compensatory top-down control. SZP reaching a higher level of connectivity were able to perform better in response inhibition, whereas in HC a strong increase in ISPC may reflect an overly activated cognitive control system, which is detrimental to task performance.