The aim of this study was to examine neurophysiological and behavioral correlates of cognitive control elicited by a modified flanker task while exercising at low and moderate intensities. A secondary aim was to examine cognitive control processes at several time points during an acute bout of exercise to determine whether cognition is selectively influenced by the duration of exercise. Twenty-seven healthy participants completed a modified version of the Eriksen flanker task while exercising on a cycle ergometer at 40% and 60% VO2 peak and during a no-exercise seated control across three separate days. During task performance, continuous EEG was collected to assess neurocognitive function using the N2 and P3 event-related brain potentials (ERPs). Neurocognitive performance was assessed at 5, 15, and 25 min time points during steady-state exercise. Regardless of intensity, behavioral findings revealed impaired accuracy during both exercise conditions for the flanker task trials that require greater cognitive control. However, faster reaction times were found during moderate-intensity exercise. Neuroelectric measures revealed increased N2 and P3 amplitudes during both exercise conditions relative to rest. Together, these findings suggest divergent effects of exercise on behavioral performance measures accompanied by an upregulation of cognitive control during aerobic exercise. These impairments are discussed in terms of dual-task paradigms and the transient hypofrontality theory.