Power converters are crucial components of the wind turbine generator system (WTGS), and the reliability of wind power converters is susceptible to power fluctuations of the WTGS. The accurate lifetime estimation of power semiconductors should consider the long-time mission profiles of the WTGS. However, the existing junction temperature calculation methods don’t meet the requirement for performance of accuracy and speed. Therefore, this paper proposes a junction temperature calculation method for insulated gate bipolar transistor (IGBT). The proposed method calculates the switching cycle junction temperature of IGBT modules based on the electro-thermal analogy, then the entire fundamental frequency junction temperature are obtained iteratively via consecutive switching cycles. Performance of accuracy and speed of the proposed method is evaluated through a case study of a 1.8 MW wind power converter. Performance comparison of the proposed method with the electrical-thermal simulation and the analytical calculation is also conducted. Results show that the proposed method ensures the calculation accuracy as the electrical-thermal simulation, but greatly reduces the computational time in comparison to the electro-thermal simulation method. This proposed method can be applied in the lifetime estimation of power semiconductors considering a long time mission profiles.