Arousal level changes constantly and it has a profound influence on performance during everyday activities. Fluctuations in arousal are regulated by the autonomic nervous system, which is mainly controlled by the balanced activity of the parasympathetic and sympathetic systems, commonly indexed by heart rate (HR) and galvanic skin response (GSR), respectively. Although a growing number of studies have used pupil size to indicate the level of arousal, research that directly examines the relationship between pupil size and HR or GSR is limited. The goal of this study was to understand how pupil size is modulated by autonomic arousal. Human participants fixated various emotional face stimuli, of which low-level visual properties were carefully controlled, while their pupil size, HR, GSR, and eye position were recorded simultaneously. We hypothesized that a positive correlation between pupil size and HR or GSR would be observed both before and after face presentation. Trial-by-trial positive correlations between pupil diameter and HR and GSR were found before face presentation, with larger pupil diameter observed on trials with higher HR or GSR. However, task-evoked pupil responses after face presentation only correlated with HR. Overall, these results demonstrated a trial-by-trial relationship between pupil size and HR or GSR, suggesting that pupil size can be used as an index for arousal level involuntarily regulated by the autonomic nervous system.