The grey-headed tanager was formally described in 1825 by the German naturalist Johann Baptist von Spix under the binomial name Tanagra penicillata.

[2] Spix did not specify a type locality but this was later designated as Fonte Boa in the Brazilian state of Amazonas.

[3] The grey-headed tanager is now the only species placed in the genus Eucometis that was introduced by the English zoologist Philip Sclater in 1856.

[3][4][5] The genus name is derived from Ancient Greek eukomēs meaning "with lovely hair".

The specific epithet penicillata is from the Latin diminutive of peniculus meaning "brush".