Controllable design and synthesis of catalysts with the target active sites are extremely important for their applications such as for the oxygen reduction reaction (ORR) in fuel cells. However, the controllably synthesizing electrocatalysts with a single type of active site still remains a grand challenge. In this study, we developed a facile and scalable method for fabricating highly efficient ORR electrocatalysts with sole atomic Fe–N4 species as the active site. Herein, the use of cost-effective highly porous carbon as the support not only could avoid the aggregation of the atomic Fe species but also a feasible approach to reduce the catalyst cost. The obtained atomic Fe–N4 in activated carbon (aFe@AC) shows excellent ORR activity. Its half-wave potential is 59 mV more negative but 47 mV more positive than that of the commercial Pt/C in acidic and alkaline electrolytes, respectively. The full cell performance test results show that the aFe@AC sample is a promising candidate for direct methanol fuel cells. This study provides a general method to prepare catalysts with a certain type of active site and definite numbers.