Hypoxic-ischemic HI injury at the time of birth could lead to severe neurological dysfunction at an older age. Therapeutic hypothermia can be used to treat HI if severity of injury is determined within 6 hours of birth. EEG is generally used to assess the brain injury but it is neither widely recorded after birth nor is the expertise to interpret it commonly available. This study presents a novel system to classify HI injury using heart rate variability. The system makes decisions based on long-term statistical features extracted from the short-term HRV features. The preliminary results show the promising performance and robustness of the proposed method given a poor quality dataset. This tool can serve as decision support system in remote maternity units to help clinical staff to initiate hypothermia.