This work is part of a continued research aimed at the understanding of the promoting role of Se in the enhancement of the electrocatalytic activity of Ru in the oxygen reduction reaction. The objective of this paper is to systematically investigate the transformation of Ru nanoparticles upon their modification with the increasing amounts of Se. The Se-modified Ru/C samples with Se:Ru ratio from 0 to 1 were prepared by reacting carbon-supported Ru nanoparticles with SeO2 followed by reductive annealing and characterized using high-resolution transmission electron microscopy, energy-dispersive X-ray, X-ray diffraction analysis, X-ray photoelectron spectroscopy, and extended X-ray absorption fine structure. The results suggest that Se strongly interacts with Ru, resulting in the chemical bond between Ru and Se and formation of Ru selenide clusters whose core at low Se content can be described as Ru2Se2O0.5. At Se:Ru = 1, high-resolution electron microscopy shows evidence of formation of core-shell particles, comprising a hexagonally packed Ru core and a Ru selenide shell with lamellar morphology. Modification of Ru nanoparticles with Se enhances their electrocatalytic activity in the oxygen reduction reaction, which is explained by the role of Se in inhibiting surface oxidation.