A processing flow is proposed to suppress the severe clutter in high pulse repetition frequency (PRF) stepped-frequency radar. Firstly, the folded clutter caused by high PRF is attenuated by the intermediate frequency (IF) band-pass filter in the receiver's foreside. Secondly, two methods are brought forward to reject the residual clutter for targets of different velocities in signal processing system. On condition of specific waveform parameters, high range resolution processing eliminates the effect of the clutter to high speed targets. Two high resolution range profiles (HRRP) are utilized to cancel the clutter for low speed targets. The current method of processing need not change the basic stepped-frequency waveform and has the advantages of simplicity and effectiveness. The simulation and experiment results validate the correctness of the method.