A signal denoising method is presented for ferromagnetic material pulsed eddy current (PEC) testing signal. The method firstly performs multiple measurements, and obtains an averaged signal and then transforms the averaged PEC signal from Cartesian domain to double logarithmic domain by the developed algorithm. A median filtering process is then performed for double logarithmic domain signal. An invert transform is optional to be performed to transform the processed signal from double logarithmic domain back to Cartesian domain. A signal-to-noise ratio (SNR) improvement quantification method is applied to evaluate the SNR improvement. The performance of the method is then verified by experiments. The effects of signal averaging number and median filter’s order are discussed. Experiment results show the method is able to increase SNR by about 40dB.