Low temperature fuel cells have been developed as next-generation, clean energy conversion devices. Oxygen reduction reaction (ORR), which is one of the biggest barrier in low temperature fuel cells, is more facile in alkaline media than acidic media. Therefore, anion exchange membrane fuel cells (AEMFCs) have been garnering attention. In AEMFCs, it could be possible that the use of less-expensive ORR electrocatalysts such as metal-free catalysts based on heteroatom doped carbon materials. To realize the feasibility of metal-free catalysts, studies based on membrane electrode assemblies (MEA) are important but most of previous studies are focused on kinetic activities in half-cell measurement systems. Herein, we report the effects of pore size and doping site Position of metal-free ORR electrocatalysts in MEAs using well-defined ordered mesoporous materials. Pore size and doping-site position were precisely controlled via using different templates and size of doping precursors, separately. They affect the accessibility of reactants to reaction sites, which influences mass-transport properties and the utilization of doping-sites. As a result, remarkable on-set potential and maximum power density were obtained by the MEA using a large pore sized- N, P co-doped ordered mesoporous carbon with controlled doping-site position as a cathode catalyst. It is expected that the effective design strategy of electrocatalysts developed in this work could be widely applied to various electrocatalytic systems in addition to AEMFCs.