In this study, we explored the effect of interlayers between ZnO layer and active layer on the performance of inverted organic photovoltaic cells by employing fluorene-based conjugated poly-electrolytes (CPE) with different side chains. Poly[9,9'-bis(6''-N,N,N-trimethylammoniumhexyl) fluorene-alt-1,4-phenylene dibromide] (P1) and poly[(9,9'-bis(4-(6-N, N, N-trimethylammoniumhexyloxy) phenyl)fluorene-2,7-diyl)-alt-1,4-phenylene dibromide] (P2) were synthesized and used as interlayers in inverted organic photovoltaic cells. We fabricated organic photovoltaic devices with the following structure: ITO/ZnO/CPE/active layer/MoO3/Ag. The CPE was applied between the ZnO layer and active layer, which comprised poly[4,8-bis-(5-(2-ethylhexylthio) thiophen2- yl) benzo[1,2-b: 4,5-b']-dithiophene] (PBDTT-S) and PC71BM. We confirmed the changes in the work functions of ZnO using ultraviolet photoelectron spectroscopy. The measured work functions of ZnO were -4.32 and -4.21 eV when P1 and P2 were used as the interlayer, respectively; these values are slightly higher than that of bare ZnO (-4.42 eV). One of the devices fabricated with P2 showed a maximum power conversion efficiency of 4.37%, which is higher than that of the device without a CPE interlayer (3.76%).