Intermittent intensity clutter in wind profiling radar severely interferes with the identification and spectrum estimation of atmospheric echo signals. In order to remove such clutter, a method based on Fractional Fourier transform (FrFT) is presented. The proposed method makes use of energy concentration property of intermittent clutter in fractional Fourier frequency domain. Not only the intermittent intensity clutter can be removed in the fractional Fourier frequency domain by using a narrow band-stop filter, but also the atmospheric signal in the time domain can be reconstructed after removing the clutter. Computer simulations have verified the effectiveness of the method.