Apparatus for and methods of core cooling the blood of an equine animal. The apparatus is a flexible boot with an orthotic pad that has various features to allow for circulating coolant so the bottom hoof area of an equine can be cooled. Optionally the pad is designed to allow cooling under vacuum. In some aspects the apparatus also provides elements to facilitate cooling the lower leg of the equine in a way designed to allow coolant circulated through the boot pad to also be circulated through leg cooling elements while maintaining a controlled temperature against the leg surface. The invention is also a method of core cooling an animal utilizing the apparatus described.