The 24-hour rhythm of core body temperature (CBT) is commonly used in humans as a tool to assess the oscillation of the central endogenous circadian pacemaker. The invasive nature of the rectal sensor used to collect CBT makes it difficult to use in ambulatory conditions. Here we validate the use of a newly developed brain temperature (BT) sensor against that of a standard rectal temperature sensor using a 72-hour ultra-rapid sleep-wake (URSW) cycle procedure. A significant circadian variation of both body temperature recordings was observed from which a phase and amplitude was reliably determined. These results indicate that BT can be refined as a non-invasive alternative to CBT measurements in the evaluation of circadian phase in field conditions.