The failure to regulate one’s own emotions, that is Emotional Dysregulation (ED), has become a diagnostic challenge in the last decades with a great heterogeneity of presentations, and has been recently considered a core dimension of psychopathology in youths in a transnosographic conceptualization. Peripheral indexes of functioning of the autonomic nervous system (ANS) activity emerged as reliable transdiagnostic biomarkers of psychopathology, since arousal has been frequently found to be dysregulated in individuals with ED. For these reasons, the present study aimed to identify the ANS functioning correlates of affective reactivity to emotionally salient videoclips in a stimulation protocol conducted on a clinical sample of youths. To this aim, 30 subjects (mean age: 13.93 ± 11.74) were recruited and presented with videoclips showing emotional content (joy, fear, anger, sadness, and anger). Before (Baseline), during (Task) and after (Recovery) the registration, electrocardiogram and electrodermal activity were recorded using wearable technologies. Several indices related to the activation of sympathetic and parasympathetic nervous system were extracted. These indices were compared among the different phases and emotions and correlated with clinical measures. Results showed that some emotions are more able to elicit ANS response than other and that there is a correlation between physiological activation and clinical profile. The results of the present study help to elucidate the mechanisms of ED in psychopathology and can be useful to guide behavioral as well as pharmacological treatment.