Filterbanks have been widely used in the field of multi-channel signal processing for their simple efficient implementation architectures. Especially, the polyphase DFT(Discrete Fourier Transform) filterbank is the most preferred filterbank for the uniform spaced multi-channel processing due to its simplicity. In frequency hopped communication systems, however, the use of the polyphase DFT filterbank is limited due to its undesirable transient response from hop-to-hop transitions. In this paper, the transient response of polyphase DFT filterbanks in the hop-to-hop transition was analyzed, and the efficient methods to overcome such a problem was proposed. Simulation results showed that the proposed schemes could resolve this issue efficiently.