Notothenia cyanobrancha was first formally described in 1844 by the Scottish naval surgeon, naturalist and Arctic explorer John Richardson with the type locality given as Kerguelen Island.

However, more research is needed to determine whether this species should be placed in its own genus; as of 2021, FishBase considers Indonotothenia cyanobrancha a junior synonym of N.

[4][5][6] The specific name is a compound of cyano meaning "blue" and branchus which means "gill", a reference to the band of deep purple or blue colour skirting the edge of the gill membrane.

The margin of the opercular membrane (near the gills) is distinctively dark blue, hence the name of this species.

[4][6] These hatch into larvae with a year-long pelagic phase that are the most abundant inshore larval fish species around the Kerguelen Islands, where they are present year-round, but most common in February.