Objectives Cognitive control is an adaptive behavior that requires goal-maintaining ability in response to a dynamically changing environment. This study examined the differences and profiles of cognitive control deficits to determine if cognitive control could be a possible candidate as a common pathophysiologic marker of schizophrenia and bipolar disorder. Methods Three groups were included in this study: remitted schizophrenia patients (n=56), patients in euthymic states of bipolar I disorder (n=52), and healthy control (n=57), who were matched on sex, age, years of education. The Continuous Performance Test of the AX version (AXCPT) was used to evaluate the cognitive control function. Intelligence, psychopathology, and psychomotor speed were also examined. The degree of cognitive control deficits was assessed by the commission error rates, correct response times, and the d’ values. Results Both patient groups performed worse in the AX and BX trials than the healthy control. Both patient groups showed a delayed response in all trials than the healthy control. The d’ value was the highest in the healthy control group, but there were no significant differences between the two patient groups. The profile of defects in the two patient groups was the same, with the BX trial having the highest defects in the order of the AX, BY, and AY trials. Conclusion These findings indicate that cognitive control is impaired in patients with schizophrenia and bipolar I disorder. Impairments in cognitive control are likely to be a possible shared pathophysiological marker for both disorders.