Hypothermia, especially applied during ischemia, is the gold-standard neuroprotectant. When delayed, cooling must often be maintained for a day or more to achieve robust, permanent protection. Most animal and clinical studies use whole-body cooling-an arduous technique that can cause systemic complications. Brain-selective cooling may avoid such problems. Thus, in this rat study, we used a method that cools one hemisphere without affecting the contralateral side or the body. Localized brain hypothermia was achieved by flushing cold water through a metal tube attached to the rats' skull. First, in anesthetized rats we measured temperature in the cooled and contralateral hemisphere to demonstrate selective unilateral cooling. Subsequent telemetry recordings in awake rats confirmed that brain cooling did not cause systemic hypothermia during prolonged treatment. Additionally, we subjected rats to transient global ischemia and after recovering from anesthesia they remained at normothermia or had their right hemisphere cooled for 2 days (∼32°C-33°C). Hypothermia significantly lessened CA1 injury and microglia activation on the right side at 1 and 4 week survival times. Near-complete injury and a strong microglia response occurred in the left (normothermic) hippocampus as occurred in both hippocampi of the untreated group. Thus, this focal cooling method is suitable for evaluating the efficacy and mechanisms of hypothermic neuroprotection in global ischemia models. This method also has advantages over many current systemic cooling protocols in rodents, namely: (1) lower cost, (2) simplicity, (3) safety and suitability for long-term cooling, and (4) an internal control-the normothermic hemisphere.