Foliar spray with selenium salts can be used to fortify tomatoes, but the results vary in relation to the Se concentration and the plant developmental stage. The effects of foliar spraying with sodium selenate at concentrations of 0, 1, and 1.5 mg Se L-1 at flowering and fruit immature green stage on Se accumulation and quality traits of tomatoes at ripening were investigated. Selenium accumulated up to 0.95 µg 100 g FW-1, with no significant difference between the two concentrations used in fruit of the first truss. The treatment performed at the flowering stage resulted in a higher selenium concentration compared to the immature green treatment in the fruit of the second truss. Cu, Zn, K, and Ca content was slightly modified by Se application, with no decrease in fruit quality. When applied at the immature green stage, Se reduced the incidence of blossom-end rot. A group of volatile organic compounds (2-phenylethyl alcohol, guaiacol, (E)-2-heptenal, 1-penten-3-one and (E)-2-pentenal), positively correlated with consumer liking and flavor intensity, increased following Se treatment. These findings indicate that foliar spraying, particularly if performed at flowering stage, is an efficient method to enrich tomatoes with Se, also resulting in positive changes in fruit aroma profile.