The fixed analyzer method commonly used for measuring the polarization mode dispersion of optical fibers can introduce errors and reduce measurement accuracy, and thus a novel scheme based on wavelet threshold denoising is proposed to further improve the measurement accuracy. The specific workflow of the scheme is presented and the selection principle and scheme of wavelet threshold, threshold function, mother wavelet and wavelet decomposition layer number are discussed in detail. An experimental platform is built and the measurement is conducted. The measurement results are compared with those by the commonly used Fourier transform method and commercial polarization mode dispersion measurement instruments. The experimental results show that the proposed wavelet threshold denoising scheme can be used to effectively reduce the impact of noises on the measurement results and is also suitable for different types and lengths of test fiber samples. If the measurement results by commercial instruments are taken as the reference standard, the maximum error by the proposed scheme is 2.27%, which indicates the polarization mode dispersion measurement accuracy by the fixed analyzer method is significantly enhanced.