Rett Syndrome (RTT) is a complex neurodevelopmental disorder that has multi-system involvement with co-occurring epilepsy, breathing problems and autonomic dysregulation. Autonomic dysregulation can increase the risk of cardiorespiratory vulnerability in this patient group. Assessment of heart rate variability (HRV) provides an overview of autonomic health in RTT and offers insight into how the sympathetic and parasympathetic components of the nervous system function. However, to our knowledge, no study has evaluated HRV in Rett patients to assess how the dynamics of autonomic function vary with age and changes during the day and/or night. Using non-invasive wearable sensors, we measured HRV in 45 patients with RTT and examined the time and frequency domain sympathetic and parasympathetic indices. Among the HRV indices assessed, heart rate decreases with age and is lower in the night across all ages studied. The sympathetic index (SDNN) and the parasympathetic indices (RMSSD and pNN50) are not seen to change with age. Nevertheless, these indices were all higher during the day when compared to the night. Our findings appear to show that Rett patients are less adaptable to autonomic changes during the night. In the clinical setting, this might be more relevant for patients with severe psychopathology.