Due to the Fenton reaction, the presence of Fe and peroxide in electrodes generates free radicals causing serious degradation of the organic ionomer and the membrane. Pt-free and Fe-free cathode catalysts therefore are urgently needed for durable and inexpensive proton exchange membrane fuel cells (PEMFCs). Herein, a high-performance nitrogen-coordinated single Co atom catalyst is derived from Co-doped metal-organic frameworks (MOFs) through a one-step thermal activation. Aberration-corrected electron microscopy combined with X-ray absorption spectroscopy virtually verifies the CoN<sub>4</sub> coordination at an atomic level in the catalysts. Through investigating effects of Co doping contents and thermal activation temperature, an atomically Co site dispersed catalyst with optimal chemical and structural properties has achieved respectable activity and stability for the oxygen reduction reaction (ORR) in challenging acidic media (e.g., half-wave potential of 0.80 V vs reversible hydrogen electrode (RHE). The performance is comparable to Fe-based catalysts and 60 mV lower than Pt/C -60 μg Pt cm<sup>-2</sup> ). Fuel cell tests confirm that catalyst activity and stability can translate to high-performance cathodes in PEMFCs. The remarkably enhanced ORR performance is attributed to the presence of well-dispersed CoN<sub>4</sub> active sites embedded in 3D porous MOF-derived carbon particles, omitting any inactive Co aggregates.