Fast and accurate calculation of junction temperature is attractive for reliability evaluation of insulated gate bipolar transistor(IGBT) module. However, in most of existing methods, a trade-off between calculation accuracy and computational burden should be made. Considering this, a fast junction temperature calculation method based on the Fourier transform is proposed in this paper, which has the ability of maintaining an acceptable accuracy. In this method, the Fourier transform is applied in the instantaneous phase current, and the current is expressed by continuous Fourier components. Then, the power loss of the IGBT module is quantified with a description of temporal and continuous. With the assistance of the thermal network model, the dynamics of junction temperature within a fundamental period are expressed analytically. Finally, the effectiveness of the proposed junction temperature calculation method is verified through extensive simulations and experimental tests.