This paper presents a miniaturized brain cortex cooling device and system using thermoelectric (TE) cooler for hypothermia therapy application on freely moving rat. Two type of cooling electrodes including planar and micro-needle structures are fabricated and studied by EEG recording. Comparing to prior arts, our approach can be applied under freely moving behavior. The cooling temperature is designed as 2°C to avoid permanent injury in brain. Packaged planar or needle electrode with TE cooler consumes only 2×2mm2. EEG recording electrodes and thermocouple are implanted for observation as well. Simulation result shows that TE-cooler with needle type electrode behaves deeper effective cooling depth and faster cooling response in rodent cortex range (∼2mm deep). Long term EEG monitoring on freely moving rat also presents no extra side effects with continuously cooling.