Simple SummaryDuring exercise, horses produce heat from working muscles, and this heat, under certain circumstances, may accumulate in the body. Conduction, convection, radiation, and evaporation are the primary heat transfer mechanisms for the control of body temperature. Horses that undergo strenuous exercise in hot and humid environments may have heat production that exceeds their ability to dissipate the heat. Therefore, the horse could be at risk from postexercise exertional heat illness, possibly leading to heat shock and death. To avoid this outcome, many Thoroughbred racehorses are cooled-down postracing by using water application (ice-cold water or ambient temperature water), fans, combinations of water application and fans, or water application followed by scraping the water off the horse. Early detection of the clinical signs of exertional heat illness and adequate treatments are important to prevent severe hyperthermia and irreversible thermal damage. The development and application of technology that will provide accurate, rapid, safe, and noninvasive monitoring of body temperature changes might help the detection of postrace exertional heat illness in equine athletes. Implanted percutaneous thermal sensing microchip (PTSM) is a reliable method to measure body temperature in horses; however, the optimal location within the body of the horse needs to be determined.Accurately measuring body temperature in horses will improve the management of horses suffering from or being at risk of developing postrace exertional heat illness. PTSM has the potential for measuring body temperature accurately, safely, rapidly, and noninvasively. This study was undertaken to investigate the relation between the core body temperature and PTSM temperatures prior to, during, and immediately after exercise. The microchips were implanted into the nuchal ligament, the right splenius, gluteal, and pectoral muscles, and these locations were then compared with the central venous temperature, which is considered to be the “gold standard” for assessing core body temperature. The changes in temperature of each implant in the horses were evaluated in each phase (prior to, during, and immediately postexercise) and combining all phases. There were strong positive correlations ranging from 0.82 to 0.94 (p < 0.001) of all the muscle sites with the central venous temperature when combining all the phases. Additionally, during the whole period, PTSM had narrow limits of agreement (LOA) with central venous temperature, which inferred that PTSM is essentially equivalent in measuring horse body temperature. Overall, the pectoral PTSM provided a valid estimation of the core body temperature.