We report the structure-controlled synthesis of FePt/MgO NPs and their catalysis for oxygen reduction reaction (ORR) in 0.5 M H2SO4 solution. The synthesis yields fcc-FePt/MgO and fct-FePt/MgO NPs with the MgO coating being readily removed for catalytic studies. The fct-FePt NPs show higher activity and durability than the fcc-FePt in the ORR condition. The results indicate that the fully ordered fct-FePt could serve as a practical Pt-based catalyst for fuel cell applications.