Demand on the practical synthetic approach to the high performance electrocatalyst is rapidly increasing for fuel cell commercialization. Here we present a synthesis of highly durable and active intermetallic ordered face-centered tetragonal (fct)-PtFe nanoparticles (NPs) coated with a "dual purpose" N-doped carbon shell. Ordered fct-PtFe NPs with the size of only a few nanometers are obtained by thermal annealing of polydopamine-coated PtFe NPs, and the N-doped carbon shell that is in situ formed from dopamine coating could effectively prevent the coalescence of NPs. This carbon shell also protects the NPs from detachment and agglomeration as well as dissolution throughout the harsh fuel cell operating conditions. By controlling the thickness of the shell below 1 nm, we achieved excellent protection of the NPs as well as high catalytic activity, as the thin carbon shell is highly permeable for the reactant molecules. Our ordered fct-PtFe/C nanocatalyst coated with an N-doped carbon shell shows 11.4 times-higher mass activity and 10.5 times-higher specific activity than commercial Pt/C catalyst. Moreover, we accomplished the long-term stability in membrane electrode assembly (MEA) for 100 h without significant activity loss. From in situ XANES, EDS, and first-principles calculations, we confirmed that an ordered fct-PtFe structure is critical for the long-term stability of our nanocatalyst. This strategy utilizing an N-doped carbon shell for obtaining a small ordered-fct PtFe nanocatalyst as well as protecting the catalyst during fuel cell cycling is expected to open a new simple and effective route for the commercialization of fuel cells.