Adaptive behavior depends on the ability to effectively regulate emotional responses. Continuous failure in the regulation of emotions can lead to heightened physiological reactions and to various psychopathologies. Recently, several behavioral and neuroimaging studies showed that exertion of executive control modulates emotion. Executive control is a high-order operation involved in goal-directed behavior, especially in the face of distractors or temptations. However, the role of executive control in regulating emotion-related physiological reactions is unknown. Here we show that exercise of executive control modulates reactivity of both the sympathetic and the parasympathetic components of the autonomic nervous system. Specifically, we demonstrate that both pupillary light reflex and pupil dilation for aversive stimuli are attenuated following recruitment of executive control. These findings offer new insights into the very basic mechanisms of emotion processing and regulation, and can lead to novel interventions for people suffering from emotion dysregulation psychopathologies.