Intrusive cognitions are a natural occurrence within our stream of consciousness, however, when they become repetitive, negative, distressing, and difficult to control, they may warrant clinical concern. Thought suppression is a common control strategy used to manage intrusive thoughts even though research suggests it may actually exacerbate the problem. Conversely, acceptance-based interventions have gained recent attention as an alternative strategy for managing distressing internal experiences. Only preliminary research has focused on the psycho- and neurophysiological bases of intrusive cognitions, and their relationship to cognitive control strategies. Evidence suggests that the anterior cingulate cortex (ACC) may be a brain region critically involved in this process. The present investigation compared the subjective, behavioral, and physiological effects of a thought suppression and acceptance strategy in a sample of university students with high or low obsessive-compulsive (OC) characteristics who were exposed to an emotion-evoking film clip. Participants were instructed either to suppress or accept any intrusive cognitions during a rest period after the film clip, while monitoring for the number of intrusions. Next, psychophysiological signals and reaction times were measured while participants performed a variant of the Stroop task. The commission of errors during a forced choice task generates an error-related negativity (ERN), which is believed to index activity in the ACC. Results showed that self-reported intrusions during the rest interval were greater for the acceptance group and the high-OC group. Correlations suggested that participants who reported more effort at suppression also indicated more distress about their thoughts, whereas those who reported more acceptance indicated less distress. During Stroop task errors, the ERN was apparent as a maximal frontal negativity, and was larger for the suppression group than the acceptance group at a frontal scalp site (Fz), but not a central scalp site (Cz). Correlations between self-reported intrusions at rest and ERN amplitude indicated that participants who reported fewer intrusions demonstrated enhanced ERNs, a marker for increased ACC activity. These findings may be interpreted as supporting the hypothesis that thought suppression is associated with increased ACC activity and greater self-reported discomfort with the intrusions.