The development of non-precious metal oxygen reduction catalysts is vital for enabling the commercialization of proton exchange membrane fuel cells, and Fe/N/C catalysts prepared by the pyrolysis of Fe, N, and C-containing precursors have been widely studied for this purpose. The role of atomically dispersed Fe centers in the reaction mechanisms of Fe/N/C catalysts has been widely studied. This paper demonstrates a facile magnetic purification approach for obtaining atomically dispersed Fe centers for conducting superior Fe/N/C catalysis. Upon treatment of a Fe/N/C catalyst prepared by pyrolyzing Fe-containing polyimide nanoparticles with a magnet, the clustered Fe species (metallic Fe and Fe3C) observed before the purification were successfully eliminated, and atomically dispersed Fe species were clearly observed by microscopy. Comparison of the oxygen reduction activities of the Fe/N/C catalysts before and after the magnetic purification in half-cell and fuel cell testing revealed the retention of the high catalytic performances of the Fe/N/C catalysts. Furthermore, no loss in catalytic performance or durability was observed after the magnetic purification.