It is a recently described plant, previously included with P. fitzgeraldii, but distinguished from that species by its greenish-brown flowers with their white labellum and narrower brown callus.

Prasophyllum stygium is a terrestrial, perennial, deciduous, herb with an underground tuber and a single tube-shaped, shiny, pale green leaf which is 150–200 mm (6–8 in) long and 2–4 mm (0.08–0.2 in) wide at its maroon base.

[2][3] Prasophyllum stygium was first formally described in 2017 by David Jones and Dean Rouse and the description was published in Australian Orchid Review from a specimen collected in the Deep Lead Nature Conservation Reserve near Stawell.

[1] The specific epithet (stygium) is a Latin word meaning "stygian" after the mythological river Styx,[4] referring to the type location, a former mining area where gold was extracted from buried river beds.

[2] The elfin leek orchid is only known from about thirty plants growing in forest at the type location.