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A method to calibrate classical heat flux sensors is presented. The classical approach to measure the temperature inside a known material by using a thermocouple fails when the measurement time is very short. In this work the surface heat flux is determined by solving the inverse heat conduction problem using a noninteger identified system as a direct model for the estimation process. Using short pulse laser calibration measurements the crucial design aspects of the sensor that play a significant role when assuming one-dimensional, semi-infinite heat transfer have been accounted for. The theoretical approach as well as the calibration results are presented and comparisons to the classical approach and results from finite element modeling are shown. It is concluded that the new method ameliorate the heat flux sensor significantly and extend its application to very short measurement times.