A computer-aided synthesis technique for E-septum bandpass filters with improved stopband and spurious mode rejection performance is developed. This design is based on field expansion into suitably normalized eigen-modes which yields directly the modal S-matrix. Higher order mode excitation and finite thickness of inserts are included in the calculations. The analysis results of proposed structure show the improvement of stopband performance and reduction of filter dimensions compared with conventional E-septum bandpass filter. The validity of the analysis results are confirmed by the HFSS. The computing time of our proposed method is decreased dramatically comparing with the HFSS.