The optimization of catalyst layer activity is essential for PEFCs to improve their performance. In this study, the relation between the structure of the nanofiber catalyst layer and catalyst layer activity, which includes reactivity and diffusivity, was examined. Carbon-alloy nanofiber, which is alloyed with nitrogen atoms and Pt free catalyst for oxygen reduction reaction, was used for the cathode catalyst. Four catalyst layers of nanofiber catalyst in different lengths from 0.80 to 6.4 mu m were prepared and their performances in a half cell and membrane electrode assembly (MEA) were evaluated. The bulky catalyst layer with an increased pore volume at the large secondary pore size larger than 2 mu m was formed with the longer catalyst. The MEA with the longer catalyst showed a higher performance. The bulky catalyst layer by using the longer catalyst can provide a higher utilization of the active sites and also promote mass transport.