The rufous-gaped hillstar was formally described in 1851 by the French ornithologist Jules Bourcier based on a specimen that he had collected in Ecuador.

The specific epithet bougueri was chosen to honour the French mathematician Pierre Bouguer who had visited Peru in 1736–1742.

"[9] The rufous-gaped hillstar is found on the Pacific slope of the Andes from Colombia's Chocó Department south into Ecuador as far as Pichincha Province.

[9] The rufous-gaped hillstar usually forages in the lower and middle strata of the forest but occasionally in the canopy.

[9] The rufous-gaped hillstar's breeding season in Colombia spans from December to March; it has not been documented in Ecuador.

It builds a cup nest of moss and lichen on a vertical branch, typically 8 to 12 m (26 to 39 ft) high in a tall tree.

[1] It is considered uncommon to rare in Ecuador and fairly common in Colombia, and occurs in at least two protected areas in the latter.