The inability to regulate excessive drinking despite negative consequences is a defining characteristic of alcohol use disorder (AUD). Neuroimaging studies of AUD have reported attenuated activity in the prefrontal cortex which is suggestive of cognitive control deficits. Reduced prefrontal activity may underlie impaired self-control and contribute to the development and maintenance of AUD. Despite the evidence of increasing rates of alcohol misuse among women, neuroimaging studies probing cognitive control in men compared to women with AUD are lacking. Archival data obtained from 100 participants (age=51.42±12.3) were analyzed as a function of their AUD history and gender. A total of abstinent 52 individuals (29 men) had a history of AUD and high-intensity drinking for five or more years. They were demographically matched with 48 non-AUD control (CTL) participants (23 men). Functional magnetic resonance imaging (fMRI) scans were obtained during a modified version of the Eriksen Flanker task which elicits perceptual- vs response-level conflict. Behavioral and imaging data were analyzed with a mixed 2 (Group) x 2 (Gender) x 3 (Task) ANOVA, followed by lower-level analyses. Additionally, correlation analyses examined associations between neurobehavioral indices and drinking-related variables, personality traits, and neuropsychological measures. Even though the task successfully induced response conflict as indicated by lower accuracy and longer reaction times, behavioral measures showed no Group or Gender differences. In contrast, the AUD group exhibited reduced brain activity to response conflict in the orbitofrontal (OFC) and posterior cingulate (PCC) cortices, the left superior frontal gyrus, (SFG), and the thalamus relative to the CTL group. Lower SFG activation was associated with higher AUDIT scores, indicative of the long-term consequences of alcohol misuse. Lower OFC activation was negatively correlated with impulsivity and negative moods. There were no main effects or interactions involving the Gender factor. In the absence of behavioral deficits, the AUD group showed attenuated BOLD activity to response conflict compared to the CTL group in regions subserving decision making, motor planning, impulse control, and reward valuation, which is indicative of impaired self-regulation. These results suggest that a history of AUD is associated with lasting neurofunctional changes during cognitive control in the prefrontal cortex.