Selenium, a group 16 (chalcogen) element, can endow metal oxides with unique properties when replacing oxygen atoms from specific sites. Polyoxometalates (POMs), a class of anionic metal oxide clusters, exhibit structure-dependent properties and applications. Despite the potential of chalcogen substitution, the replacement of oxygen atoms in POMs with chalcogens has been rarely explored. In a recent study, we demonstrated site-selective oxygen-to-sulfur substitution in the Keggin-type POM [SiW12O40]4−. Building on this, we now report the first synthesis of a polyoxoselenidotungstate, featuring terminal selenido ligands (W=Se bonds), using a site-selective oxygen-to-selenium substitution reaction. By reacting [SiW12O40]4− with Woollins’ reagent (2,4-diphenyl-1,3,2,4-diselenadiphosphetane 2,4-diselenide) in organic solvents, all twelve terminal oxido ligands (W=O) were selectively converted to selenido ligands (W=Se). The resulting compound [SiW12O28Se12]4− retains the Keggin-type framework and exhibits distinct optical and electronic properties owing to the incorporated selenium atoms. These findings pave the way for the systematic modification of oxygen sites in POMs with the heavier chalcogens sulfur, and selenium, opening new avenues for tailoring their properties and expanding their utility across diverse fields of materials science.