Photocatalytic fuel cells (PFCs) convert organic waste into electricity, thereby providing a potential solution for remediating environmental pollution and solving energy crises. Most PFCs for energy generation applications use powder photocatalysts, which have poor mechanical stability, high internal resistance, and may detach from the substrate during reactions, leading to unstable performance. Integrated photoelectrodes can overcome the drawbacks of powder catalysts. In this study, an integrated photoanode was prepared based on a silicon nanowire arrays/zinc oxide (Si NWs/ZnO) heterojunction by combining metal-assisted chemical etching (MACE) and hydrothermal methods. The resulting photoanode was used to assemble a PFC for simultaneous electricity generation and Rhodamine (RhB) dye wastewater degradation. This PFC showed excellent cell performance under irradiation, with a short-circuit current density of 0.183 Am−2, an open-circuit voltage (OCV) of 0.72 V, and a maximum power density of 0.87 W m−2. It could also be used continuously 20 times while degrading > 90% of RhB. This performance was ascribed to the three-dimensional (3D) structure and large surface area of Si NWs, as well as the matched band structure of ZnO, which facilitated the efficient separation and transport of photogenerated carriers in Si NWs/ZnO. The integrated structure also shortened the carrier transport pathways and suppressed carrier recombination. This research provides a foundation for the development of efficient, stable, low-cost, small-scale PFCs.