Fluctuations in global neural gain, arising from brainstem arousal systems, have been found to shape attention, learning, and decision-making as well as cortical state. Comparatively, little is known about how fluctuations in neural gain affect cognitive control. In the present study, we examined this question using a combination of behavioral methods, pupillometry, and computational modeling. Simulations of a comprehensive model of the Stroop task incorporating task conflict and both proactive and reactive forms of control indicated that increasing global gain led to an overall speeding of reaction times, increased Stroop interference, and decreased Stroop facilitation. Pupil analyses revealed that the pre-trial pupil derivative (i.e., rate of change), a putative non-invasive index of global gain, showed the same diagnostic relationships with the Stroop-task performance of human participants. An analysis of the internal model dynamics suggested that a gain-related increase in task conflict and corresponding (within-trial) increase in reactive control are vital for understanding this pattern of behavioral results. Indeed, a similar connectionist model without this task-conflict-control loop could not account for the results. Our study suggests that spontaneous fluctuations in neural gain can have a significant impact on reactive cognitive control.