Various mental disorders are associated with cognitive impairments affecting everyday life. When comparing patients with major depressive disorder (MDD) and schizophrenia (SZP), different severity levels of cognitive deficits can be observed. On electrophysiological level, different characteristics of frontal midline theta oscillations including inter-trial phase clustering (ITPC) were associated with initiating effective cognitive control. ITPC represents the consistency of phase angles of oscillatory processes over trials and time points. Therefore, the aim of our study was to quantify cognitive deficits in MDD and SZP and link them to the ITPC of theta-range oscillations. Hence, fourty-one MDD, thirty-two SZP and respectively matched healthy controls (HC) performed two experimental tasks (Go/NoGo, Eriksen flanker) while an electroencephalogram (EEG) was recorded. In comparison to the other two groups, SZP showed worse performance (accuracy, reaction times) in both tasks. Whereas, there was no difference between MDD and HC. Considering the EEG data, an universal modulation of ITPC in conflicting conditions (NoGo trials, incongruent trials) compared to non-conflicting conditions (Go trials, congruent trials) was only evident on a numerical level. However, compared to the other two groups, SZP showed a lower overall condition-unspecific ITPC in both tasks. Again, a significant difference between MDD and HC was absent. Taken together, these results could be interpreted within the dysconnectivity hypothesis of schizophrenia because performance deficits and changes of ITPC were unique to SZP but absent in MDD. Second, these phase synchrony disruptions in SZP underlines the relevance of an intact theta phase-synchronized information transfer to recruit cognitive control resources.