According to embodied simulation theories, others’ emotions are recognized by the unconscious mimicking of observed facial expressions, which requires the implicit activation of the motor programs that produce a specific expression. Motor responses performed during the expression of a given emotion are hypothesized to be directly linked to autonomic responses associated with that emotional behavior. We tested this hypothesis in 9 children (M_age = 5.66) affected by Moebius syndrome (MBS) and 15 control children (M_age = 6.6). MBS is a neurological congenital disorder characterized by underdevelopment of the VI and VII cranial nerves, which results in paralysis of the face. Moebius patients’ inability to produce facial expressions impairs their capacity to communicate emotions through the face. We therefore assessed Moebius children’s autonomic response to emotional stimuli (video cartoons) by means of functional infrared thermal (fIRT) imaging. Patients showed weaker temperature changes compared to controls, suggesting impaired autonomic activity. They also showed difficulties in recognizing facial emotions from static illustrations. These findings reveal that the impairment of facial movement attenuates the intensity of emotional experience, probably through the diminished activation of autonomic responses associated with emotional stimuli. The current study is the first to investigate emotional responses in MBS children, providing important insights into the role of facial expressions in emotional processing during early development.