The ruddy-breasted seedeater was formally described by the Swedish naturalist Carl Linnaeus in 1758 in the tenth edition of his Systema Naturae under the binomial name Loxia minuta. The specific epithet is from Latin minutus meaning "little" or "small". The type locality is Suriname. The ruddy-breasted seedeater is now placed in the genus Sporophila that was introduced by the German ornithologist Jean Cabanis in 1844.
