Core body temperature (CBT) is one of the useful physiological indicators that is linked to physiological changes. Wearable sensors are expected to be developed to monitor CBT easily during activities. Single heat flux method is one of the non-invasive techniques that estimates CBT by measuring heat flow changes near the skin with temperature sensors. The method requires calibrating parameters for estimating CBT in advance by comparing them with reference values obtained through another method. The invasive measurement method is generally used to obtain the reference values, which poses a challenge in terms of measurement burden. Here, we propose a new calibration method that does not require acquiring reference values. This method identifies calibration parameters based on the temperature history after the measurement probe is attached. It has been numerically and experimentally confirmed that the estimation accuracy by the method is equivalent to that of a general-purpose electronic thermometer. This outcome decreases the measurement workload in CBT measurement using the single heat flux method and significantly enhances its usability.