Adult females in the type series measure 17–20 mm (0.7–0.8 in) in snout–vent length; no males were collected.

Preserved specimens are dusky brown, apart from the blackish snout, upper eyelids, and axillary and loreal regions.

[3] Aphantophryne nana differs from Aphantophryne anulata by the absence of subarticular tubercles on the hand, but the diagnostic value of this character has been questioned because specimens from Mindanao show a variable degree of distinctiveness for this trait.

[2] The types were collected in dipterocarp forest at elevations between 550 and 910 m (1,800 and 3,000 ft) above sea level.

Shifting agriculture and illegal logging threaten its habitat at lower altitudes.