In this paper, a fractional Fourier transform (FRFT) based technique for the elimination of amplitude and phase distortions in the transmultiplexer (TMUX) is presented. The core elements of the TMUX, the synthesis and analysis filter banks cause amplitude and phase changes due to the filtering operations in the filter banks thereby altering the perfect reconstruction property. This study investigates a new approach to transmultiplexer design in the processing of the nonstationary signals.