Birth asphyxia constitutes a major global public health burden for millions of infants with a critical need for real time physiological biomarkers. This proof of concept study targets the translational rigor of such biomarkers and aims to examine whether the variability in the amplitude-integrated EEG (aEEG) outputs impact the determination of neurovascular coupling (NVC) in newborns with encephalopathy. A convenience sample with neonatal asphyxia were monitored for twenty hours in the first day of life with EEG and near infrared spectroscopy (NIRS)-based cerebral tissue oxygen saturation (SctO2). NVC between aEEG and NIRS-SctO2 was assessed using wavelet transform coherence (WTC) analysis, specifically by the wavelet total pixel number of significant coherences within 95% confidence interval. The raw EEG was converted to aEEG using three different methods: Method (M1) derives from the algorithm by Zhang and Ding. Method (M2) uses a Neonatal EEG Analysis Toolbox (WU-NEAT). Method (M3) extracts output directly from a commercial platform with an undisclosed algorithm. Our results demonstrate excellent agreement with Bland Altman comparisons for WTC-based NVC irrespective of the algorithms used, despite significant heterogeneities in the aEEG tracings produced by three algorithms. Our findings confirm the robustness of NVC wavelet analysis in Neonatal Encephalopathy related to HIE.