Empathic responses underlie our ability to share emotions and sensations with others. We investigated whether observed pupil size modulates our perception of other's emotional expressions and examined the central mechanisms modulated by incidental perception of pupil size in emotional facial expressions. We show that diminishing pupil size enhances ratings of emotional intensity and valence for sad, but not happy, angry or neutral facial expressions. This effect was associated with modulation of neural activity within cortical and subcortical regions implicated in social cognition. In an identical context, we show that the observed pupil size was mirrored by the observers’ own pupil size. This empathetic contagion engaged the brainstem pupillary control nuclei (Edinger–Westphal) in proportion to individual subject's sensitivity to this effect. These findings provide evidence that perception–action mechanisms extend to non-volitional operations of the autonomic nervous system.