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The effect of the load dependent 3rd harmonic flux on the core loss in a magnetic frequency multiplier is examined. The variation of the 3rd harmonic flux (magnitude and phase) with the loading on the multiplier is obtained using an efficient steady state simulation. A recently developed core loss model is then used to determine the effect of the load dependent flux on the losses in the device. On the basis of the harmonic loss model, it is shown that the eddy current losses can be as much as 225% larger than the losses predicted on the basis of peak flux alone.