This work discusses the heat transfer aspects of the neonate’s brain cooling process carried out by the the device to treat hypoxic-ischemic encephalopathy. This kind of hypothermic therapy is undertaken in case of improper blood circulation during delivery which causes insufficient transport of oxygen to the brain and insufficient cooling of the brain by circulating blood. The experimental setup discussed in this manuscript consists of a special water flow meter and two temperature sensors allowing to measure inlet and outlet water temperatures. Collected results of the measurements allowed to determine time histories of the heat transfer rate transferred from brain to the cooling water for three patients. These results are then analysed and compared among themselves.