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Nonlinear switched circuits are usually analyzed in the time domain. The use of frequency-domain methods to analyze the steady-state of switched circuits is usually restricted to linear circuits and, although Volterra series approaches are applied to the distortion of nonlinear switched circuits, the use of harmonic balance (HB) methods in nonlinear switched circuits seems to be marginal if not discarded. In this paper, we analyze the nonlinear class-E amplifier with an ideal switch by means of the HB method. We show how the switching function may be carefully chosen to improve the accuracy of the solution. When the circuit achieves actual class-E operation, the method converges better and is more accurate than classical time-domain methods. We conclude that the HB method is an alternative to time-domain methods that can be used to analyze the class-E amplifier in its expected operation mode.