Research into obtaining a fast, valid, reliable and non-invasive measure of core temperature is of interest in many disciplinary fields. Occupational and sports medicine research has attempted to determine a non-invasive proxy for core temperature particularly when access to participants is limited and thermal safety is of a concern due to protective encapsulating clothing, hot ambient environments and/or high endogenous heat production during athletic competition. This investigation aimed to determine the validity of inner canthus of the eye temperature (TEC) as an alternate non-invasive measure of intestinal core temperature (TC) during rest, exercise and post-exercise conditions. Twelve physically active males rested for 30 min prior to exercise, performed 60 min of aerobic exercise at 60% V̇O2max and passively recovered a further 60 min post-exercise. TEC and TC were measured at 5 min intervals during each condition. Mean differences between TEC and TC were 0.61 °C during pre-exercise, −1.78 °C during exercise and −1.00 °C during post-exercise. The reliability between the methods was low in the pre-exercise (ICC=0.49 [−0.09 to 0.82]), exercise (ICC=−0.14 [−0.65 to 0.44]) and post-exercise (ICC=−0.25 [−0.70 to 0.35]) conditions. In conclusion, poor agreement was observed between the TEC values measured through IRT and TC measured through a gastrointestinal telemetry pill. Therefore, TEC is not a valid substitute measurement to gastrointestinal telemetry pill in sports and exercise science settings.