The saffron-cowled blackbird was formally described in 1788 by the German naturalist Johann Friedrich Gmelin in his revised and expanded edition of Carl Linnaeus's Systema Naturae.

[3] Gmelin based his account on the "Troupiale jaune d'Antigue" that had been described and illustrated in 1776 by the French naturalist Pierre Sonnerat in his book Voyage à la Nouvelle Guinée.

[4] There was confusion over the origin of Sonnerat's specimen, but in 1937 Austrian ornithologist Carl Hellmayr designated Río de la Plata as the type locality.

[5][6] The saffron-cowled blackbird is now the only species placed in the genus Xanthopsar that was introduced in 1901 by the American ornithologist Robert Ridgway.

[8] A molecular genetic study has shown that the saffron-cowled blackbird is closely related to the two marshbirds in the genus Pseudoleistes.