Platinum group metal (PGM)-free catalysts that are also iron free are highly desirable for the oxygen reduction reaction (ORR) in proton-exchange membrane fuel cells, as they avoid possible Fenton reactions. Here we report an efficient ORR catalyst that consists of atomically dispersed nitrogen-coordinated single Mn sites on partially graphitic carbon (Mn-N-C). Evidence for the embedding of the atomically dispersed MnN4 moieties within the carbon surface-exposed basal planes was established by X-ray absorption spectroscopy and their dispersion was confirmed by aberration-corrected electron microscopy with atomic resolution. The Mn-N-C catalyst exhibited a half-wave potential of 0.80 V versus the reversible hydrogen electrode, approaching that of Fe-N-C catalysts, along with significantly enhanced stability in acidic media. The encouraging performance of the Mn-N-C catalyst as a PGM-free cathode was demonstrated in fuel cell tests. First-principles calculations further support the MnN4 sites as the origin of the ORR activity via a 4e− pathway in acidic media.