For the commercialization of polymer electrolyte membrane fuel cells (PEMFCs), it is essential to achieve high performance while improving the durability of the membrane electrode assembly. In particular, the durability of PEMFCs can be improved by adding radical scavengers, such as CeO2 (ceria), to the membrane. Though it is desirable to insert the ceria at the interface between the membrane and electrode, where the generated radical attack initiates, this increases interfacial resistance and ionic resistance, thereby inducing a probable reduction in initial performance, compared to that of a conventional membrane. Here, we developed modified Nafion electrolyte membranes with a spatially located patterned ceria containing Nafion ionomer to improve durability while minimizing performance degradation. The fabrication process includes an etching process to pattern the electrolyte membrane, and the ceria nanoparticle layer is selectively deposited by spray coating onto the membrane. The synergetic effect of the structural modification of the electrolyte membranes and the introduction of the functional ceria layer exhibited improved chemical durability, while maintaining the initial performance of the PEMFC.