We measured the regional saturation of oxygen of hemoglobin (rSO2) and the total hemoglobin index (HbI) in the brain and skeletal muscles of a conscious Harris’s Hawk by a near-infrared spectroscopy device (NIRS). The oxygenation levels of the breast were significantly lower than the cerebral parts. A flight exercise significantly increased the rSO2 and HbI of the breast. The breast surface temperature significantly increased in response to flight training by a thermography. NIRS enabled us to measure changes in the oxygenation levels of brain and skeletal muscles in a conscious Harris’s Hawk before and after a moving task.