The performance of proton exchange membrane fuel cells (PEMFCs) depends on the controlled size, dispersion and density of Pt nanoparticles (NPs) on carbon supports, which are strongly affected by the carbon characteristics and fabrication methods. Here, we demonstrated a high-performance Pt/carbon catalyst for PEMFCs using fluidized bed reactor atomic layer deposition (FBR-ALD) that was realized by an effective matching of the carbon supports for the FBR-ALD process and an optimization of the ionomer content during the preparation of the membrane electrode assembly (MEA). For this, the synthesis of Pt NPs was conducted on two porous supports (Vulcan XC-72R and functionalized carbon) by FBR-ALD. The functionalized carbon possessed a higher surface area with a large pore volume, abundant defects in a disordered structure and a large number of oxygen functional groups compared to those of the well-known Vulcan carbon. The favorable surface characteristics of the functionalized carbon for nucleation produced Pt particles with an increased uniformity and density and a narrow size range, which led to a higher electrochemical surface area (ECSA) than that of Pt/Vulcan carbon and commercial Pt/carbon. The PEMFC test of the respective Pt/carbon samples was investigated, and highly dense and uniform Pt/functionalized-carbon showed the highest performance through optimization of the higher ionomer content compared to that for the ALD Pt growth on Vulcan carbon and commercial Pt/carbon. In addition, the Pt catalyst using ALD demonstrated a significant long-term stability for the PEMFC. This finding demonstrates the remarkable advantages of FBR-ALD for the fabrication of Pt/carbon and the ability of functionalized carbon supports to achieve a high PEMFC efficiency and an enhanced durability.