We analyze the effect of window choice on the zero-padding method and corrected quadratically interpolated fast Fourier transform using a harmonic signal in noise at both high and low signal-to-noise ratios (SNRs) on a theoretical basis. Then, we validate the theoretical analysis using simulations. The theoretical analysis and simulation results using four traditional window functions show that the optimal window is determined depending on the SNR; the estimation errors are the smallest for the rectangular window at low SNR, the Hamming and Hanning windows at mid SNR, and the Blackman window at high SNR. In addition, we analyze the simulation results using the signal-to-noise floor ratio, which appears to be more effective than the conventional SNR in determining the optimal window.