This paper presents a novel balanced dual-band bandpass filter with in-band common-mode suppression via multiple transmission zeros from the doubly short-ended coupled line. Through the analysis of coupled line structures, the transmission zeros in the differential- and common-mode equivalent circuits are extensively studied. In differential-mode, the transmission zeros, produced by both short-ended coupled line and open stub, are independently controlled, and the desired two resonant frequencies of the dual-band bandpass filter are achieved by studying the characteristics of the doubly short-ended half-wavelength resonator. For the common-mode suppression, the intrinsic transmission zeros of short-ended coupled line in differential-mode structure appear in the same frequency locations due to the proposed common-mode strcuture. With proper adjustment of the impedances and electrical lengths of the terminated stepped-impedance resonators (SIRs) on the symmetric plane, additional transmission zeros are introduced and relocated at the differential-mode resonant frequencies, thus producing good in-band common-mode signal attenuation as highly expected. As the attractive advantage of proposed balanced structure, the common-mode performance is independent of differential-mode one. To verify the proposed design method, a prototype balanced dual-band filter is theoretically analyzed, simulated, and experimentally measured, good agreements between simulated and measured results are obtained. The measured balanced dual-band bandpass filter is centered at 900 MHz and 2.49 GHz, and in-band common-mode rejection for first and second passbands are presented with higher than 30 and 40 dB, respectively.