The golden-naped tanager was illustrated by the French naturalists Florent Prévost and Marc Athanase Parfait Oeillet Des Murs in 1842.

[4] A molecular phylogenetic study published in 2014 found that Tangara was polyphyletic and in the rearrangement to create monophyletic genera, the golden-naped tanager was moved to the resurrected genus Chalcothraupis.

[5] The genus had originally been introduced by the French naturalist Charles Lucien Bonaparte in 1851 with the golden-naped tanager as the type species.

[6] The genus name combines the Ancient Greek khalkos meaning "bronze" and thraupis, an unidentified small bird.

Juveniles of both sexes have a primarily dull blue-gray coloration with a lighter breast and belly, and lack the distinctive golden nape.