Two prominent features of obsessive-compulsive disorder (OCD) are the inability to inhibit intrusive thoughts and behaviors and pathological doubt or intolerance of uncertainty. Previous study showed that uncertain context modeled by equiprobable presentation of excitatory (Go) and inhibitory (NoGo) stimuli requires non-selective response inhibition in healthy subjects. In other words, it requires transient global inhibition triggered not only by excitatory stimuli but also by inhibitory stimuli. Meanwhile, it is unknown whether OCD patients show abnormal brain activity of the non-selective response inhibition system. In order to test this assumption, we performed an fMRI study with an equiprobable Go/NoGo task involving fourteen patients with OCD and compared them with 34 healthy controls. Patients with OCD showed pathological slowness in the Go/NoGo task. The non-selective response inhibition system in OCD included all brain areas seen in healthy controls and, in addition, involved the right anterior cingulate cortex (ACC) and the anterior insula/frontal operculum (AIFO). Moreover, a between-group comparison revealed hypoactivation of brain regions within cingulo-opercular and cortico-striato-thalamo-cortical (CSTC) circuits in OCD. Among hypoactivated areas, the right ACC and the right dorsolateral prefrontal cortex (DLPFC) were associated with non-selective inhibition. Furthermore, regression analysis showed that OCD slowness was associated with decreased activation in cingulate regions and two brain areas related to non-selective inhibition: the right DLPFC and the right inferior parietal lobule (IPL). These results suggest that non-selective response inhibition is impaired in OCD, which could be a potential explanation for a relationship between inhibitory deficits and the other remarkable characteristic of OCD known as intolerance of uncertainty.