Abstract Objective To describe early, continuous, non-invasive measures of cardiac output (CO) and evolution over time in infants with hypoxic-ischaemic encephalopathy (HIE). Study design Prospective observational study of 44 infants with HIE (23 mild, 17 moderate, 4 severe) and 17 term controls. Infants with HIE had non-invasive CO monitoring (NICOM) continuously in the neonatal unit. Term controls had NICOM recorded at 6 and 24 h. A mixed-modelling approach was used to assess change in CO over time by group. Results Infants with moderate HIE have significantly lower CO than the mild group at all timepoints (10.7 mls/kg/min lower, 95% CI:1.0,20.4, p = 0.03) which increases over time, driven by a gradual increase in stroke volume (SV). CO increased further during rewarming predominantly due to an increase in HR. Conclusion TH has a significant impact on HR but SV appears largely unaffected. NICOM may provide a non-invasive, continuous, low-cost alternative to monitoring CO in infants with HIE however further research is warranted.