Monotypic (Brewer 2010, Ridgely and Greenfield 2001a). Chapman (1924) once described a subspecies, leucogastra, from Ecuador. Todd (1929) and Hellmayr (1935) subsequently discounted leucogastra because the characters upon which it was based were matched by Colombian specimens and thus seemed to represent individual rather than geographic variation.
Rufous-naped Greenlet is a vireonid (family Vireonidae) and a member of the "canopy" greenlet clade. All members of this clade formerly were classified as species of Hylophilus, but Slager et al. (2014) documented that Hylophilus was polyphyletic, and so Slager and Klicka (2014) resurrected the genus name Pachysylvia for these species. The other members of the "canopy" greenlet clade are Pachysylvia decurtata (Lesser Greenlet), P. aurantiifrons (Golden-fronted Greenlet), P. hypoxantha (Dusky-capped Greenlet), and P. muscicapina (Buff-cheeked Greenlet) (Slager et al. 2014). The closest relative of Pachysylvia semibrunnea is Pachyslvia aurantiifrons (Slager et al. 2014).