Platinum (Pt) is the best electrocatalyst for the oxygen reduction reaction (ORR) in hydrogen fuel cells, but it is an extremely expensive resource. The successful development of a cost-effective non-Pt ORR electrocatalyst will be a breakthrough for the commercialization of hydrogen-air fuel cells. Ball milling has been used to incorporate metal and nitrogen precursors into micropores of carbon more effectively and in the direct nitrogen-doping of carbon under highly pressurized nitrogen gas in the process of the preparation of non-noble ORR catalysts. In this study, we first utilize ball milling to excavate the ORR active sites embedded in Fe-modified N-doped carbon nanofibers (Fe-N-CNFs) by pulverization. The facile ball-milling process resulted in a significant enhancement in the ORR activity and the selectivity of the Fe-N-CNFs owing to the higher exposure of the metal-based catalytically active sites. The degree of excavation of the Fe-based active sites in the Fe-N-CNFs for the ORR was investigated with cyclic voltammetry, X-ray photoelectron spectroscopy, and pore-size distribution analysis. We believe that this simple approach is useful to improve alternative ORR electrocatalysts up to the level necessary for practical applications.