In this study, polymer-coated anisotropic inorganic nanowires dispersed in PBI matrix were introduced to construct 1D proton conducting channels within PBI. Ionic-liquid and solvothermal methods were used for the synthesis of ZrO2 and W18O49 NWs, which were coated with PVPA and PDDA polymers to increase their proton conductivity. Our results showed that, prepared membranes have amorphous nature due to the dominating presence of PBI. SEM analysis revealed the average thickness of membrane of about 36 µm. TG/DTA analysis detected lower weight loss of W18O49 NWs (total 2.8%) compared to ZrO2 NWs (18%). Proton conductivity analysis showed that, PDDA/W18O49 NWs possess relatively 4 times higher proton conductivity (4$$ \times $$
×
10−4 Scm−1) compared to PDDA/ZrO2 NWs (1$$ \times $$
×
10−4 Scm−1) at 80 ℃. In addition, PDDA-coated W18O49 NWs dispersed PBI membranes showed the highest fuel cell current density (1.2 A/cm2) and power density (215 mW/cm2) at 150 ℃ after 24 h which is nearly 2.5 times higher than pure PBI membrane. In addition, they exhibited the lowest in-situ proton resistance of about (0.47 Ω) compared with that of pure PBI membrane (0.8 Ω). Our results are introducing new concepts towards the development of thin and efficient polymer electrolyte membranes for PEM fuel cells.