Mandarin pomace is a waste of the food industry that has recently been recognized as a source of various biologically valuable molecules. One of the most common compounds with biological value in mandarin pomace is pectin, which is generally widely used in the food and pharmaceutical industries. The aim of this study was to investigate the possibilities of applying the raw and purified pectin fraction of mandarin pomace in green synthesis of selenium nanoparticles. Both fractions were used in 4 different concentrations and the obtained results were compared with the results obtained using commercially available apple pectin and polyvinylpyrrolidone as a frequently used synthetic coating agent. Physico-chemical characterization of the obtained nanoparticles included measurement of zeta potential and particle size distribution using dynamic light scattering. The influence of the type/concentration of the coating agent on the total yield of green synthesis and the reductive and antiradical activity of the obtained selenium nanoparticles was also investigated. The results showed that both raw and purified pectin fraction of mandarin pomace can be considered as a suitable coating agent in green nanoparticle synthesis. Depending on the observed parameter, selenium nanoparticles obtained by encapsulation with the pectin fraction of mandarin pomace are comparable or better than selenium nanoparticles obtained by encapsulation with PVP or commercially available pectin. Further research is needed to further refine the protocol for the synthesis of selenium nanoparticles with mandarin pomace pectins as a coating agent to obtain particles with a higher antioxidant potential and a diameter of about 100 nm.