The structure of the cathode catalyst layer (CCL) is critically important for improving the performance, durability, and stability of polymer electrolyte fuel cells (PEFCs). In this study, we designed CCLs with a three-dimensional (3D) structure that could increase the surface area of the CCLs to decrease their oxygen transfer resistance. The CCLs were fabricated using an inkjet printing method, and the electrochemical performance of the CCLs in a membrane electrode assembly was evaluated using an actual cell. The results showed that at high Pt loadings, the performance of the CCL with the 3D structure was superior to that of the flat structure. In particular, at a high current density, which is related to mass transport resistance, the two structures exhibited a significant difference in performance. At a Pt loading of 0.3 mg/cm2, the CCL with the 3D structure showed the highest maximum power density among all the CCLs investigated in this study. This indicates that the 3D structure decreases the oxygen transfer resistance of the CCL. Overall, the 3D structure provided improved morphological and microstructural characteristics to the CCL for fuel cell applications.