This paper describes the preparation and characterization of proton conducting nanocomposite polymer electrolytes based a polyvinylidene fluoride-co-hexapropylene (PVDF-HFP) for protonic electrochemical cells. The electrolytes were characterized by Differential Scanning Calorimetry (DSC) and Impedance Spectroscopy (IS). It is observed that the crystallinity of the PVDF-HFP-NH4CF3SO3 system slightly increase upon addition of SiO2 nanofiller. The PVDF-HFP-NH4CF3SO3-SiO2 electrolytes reveals the existence of two conductivity maxima at 1 and 4 wt% of SiO2 concentration attributed to two percolation thresholds in the nanocomposite polymer electrolyte. The optimum value of conductivity of 1.07 × 10-3 S cm-1 is achieved for the nanocomposite polymer electrolyte film with 1 wt% SiO2. Protonic electrochemical cells was fabricated with a configuration Zn + ZnSO4.7H2O + PTFE (anode) | PVDF-HFP:NH4CF3SO3+SiO2 (electrolyte) | MnO2 + PTFE (cathode). The maximum open circuit voltage (OCV) is ~1.50 V and discharge characteristics of the cell were studied at different loads of resistances.