In this work, we present an innovative method for fabricating high-performance proton-conductive fuel cells (PCFCs) by combining magnetron sputtering and flashlight sintering (FLS) techniques. BaZr0.8Y0.2O3–δ (BZY20) electrolyte thin-films are successfully prepared by improving the crystallinity while maintaining the stoichiometry. All components of PCFC, Ni-YSZ anode, BZY20 electrolyte and Pt-GDC cathode are fabricated by sequentially sputtering them onto an AAO substrate. Electrolytic sintering is performed at 550 and 650 V conditions using FLS, effectively solving the Ba evaporation problem encountered in conventional thermal sintering methods. XRD analysis confirms that the perovskite structure is retained, and crystallinity is improved in the FLS samples. Furthermore, FE-SEM and EDS analyses confirm the uniform elemental distribution and consistent thickness of the FLS-treated electrolyte. An optimized PCFC unit cell with FLS-treated electrolyte exhibits a peak power density of 200.0 mW cm−2 at 500 °C and an ohmic resistance of 376.0 mΩ cm−2. These results suggest that the combination of magnetron sputtering and FLS techniques is a promising approach for fabricating high-performance thin-film PCFCs.