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For low frequency applications, transformer model extraction has been widely investigated using both time and frequency domain data. However, the studies for high frequency transformers have been carried out in the frequency domain only. The reason is due to the complications in acquiring time domain data for high frequency transformer model estimation. This paper presents a methodology to deal with the numerical difficulties associated with time domain data collection, and to obtain a frequency-dependent model of a 3-winding flyback transformer using time domain system identification techniques. The obtained transformer model is experimentally verified.