The structure of the cathode catalyst layer (CCL) is critically important for improved performance, durability and stability of polymer electrolyte fuel cells (PEFCs). In this research, two types of CCLs were designed for comparison, one with a 'flat structure', and one with a '3D structure', where the latter has a rough surface. An inkjet printing method was used to fabricate the structures of the cathode catalyst layer. The 3D structure was fabricated by consecutive printing and drying of single inkjet droplets. The drying of individual droplets caused a 'coffee ring effect' and multiple layers resulted in a rough surface. Results of i-V curves and impedance spectroscopy showed that electrochemical properties of the CCLs with the 3D structure were better than that of the flat structures. Overall, it is demonstrated that with a 3D structure, it is possible to achieve favorable morphological and microstructural characteristics to enhance the fuel cell performance.