Emotion dysregulation is common among individuals with autism spectrum disorder (ASD). This study examined the relationship between emotion dysregulation and resting heart rate variability (HRV), a marker of the autonomic nervous system, in ASD adolescents. Resting HRV data were collected from ASD (n = 23) and typically developing (TD) adolescents (n = 32) via short-term electrocardiogram. Parents/caregivers reported participants' level of emotion dysregulation with the Emotion Dysregulation Inventory (EDI). Controlling for the effects of age and gender, regression analyses revealed moderating effects of group, suggesting that lower resting HRV was more strongly associated with greater emotion dysregulation in ASD than TD adolescents. The results support the view that disruptions in autonomic functioning may contribute to emotion dysregulation in ASD.