Size-controlled PtRu nanoparticles embedded in TiO2 were prepared by simultaneous multi-gun sputtering from pure targets of Pt, Ru, and TiO2. The mean diameter of the PtRu nanoparticles, as confirmed by their high-resolution transmission electron microscopic images, can be varied from ∼1.8 to ∼3.7nm by changing the RF power ratio of PtRu and TiO2. The transmission electron diffraction and grazing incidence wide angle X-ray scattering patterns of the PtRu nanoparticles embedded in TiO2 confirmed that the PtRu exists as a mixed alloy structure consisting of both fcc and hcp phases, whereas the TiO2 matrix is present as an amorphous phase. The size-controlled PtRu/TiO2 electrodes were found to exhibit unique electronic properties depending on their size, which affected the potential of zero total charge and methanol oxidation reaction. The mass activity of PtRu/TiO2 for methanol oxidation was determined by the interplay of the surface electronic factors at the metal–solution-interface and the value of the oxophilicity of the nanoparticles was increased by decreasing the particle size.