The yellow-faced siskin was formally described in 1839 by the Franco-American ornithologist John James Audubon under the binomial name Carduelis yarrellii.

[4] He mistakenly specified the type locality as "Northern California" but this was re-designated in 1926 by the American ornithologist W. E. Clyde Todd as the Brazilian state of Bahia.

[5][6][7] Audubon chose the specific epithet to honour the English naturalist and bookseller William Yarrell.

[8][9] The yellow-faced siskin is now one of 20 finches placed in the genus Spinus that was introduced by Carl Ludwig Koch in 1816.

The yellow-faced siskin has a spotty distribution throughout Southeastern Brazil in the states of Ceará, Paraíba, Pernambuco, Piauí, and Bahia.