This species was described alongside K. dringi as part of a taxonomic revision of Kalophrynus nubicola from Gunung Mulu National Park, Sarawak, Malaysia (Borneo) (Fukuyama et al. 2021). All three species currently qualify as Bornean micro-endemics, reported from Gunung Mulu as their type locality, each occupying different elevational levels. The name K. puncak refers to the species’ endemism at the highest elevations of Gunung Mulu, specifically between 2110 and 2376 meters. At the lower end of this range, it overlaps with K. nubicola.

Kalophrynus puncak is a small frog. Adult males measure 19.6 to 22.7 mm in snout–vent length (SVL), while females reach 24.8 mm. The species is slightly larger than both K. nubicola and K. dringi. It lacks the yellow snout patches seen in K. nubicola, and its bluish iris and absence of dorsolateral stripes distinguish it from K. dringi. Furthermore, the skin texture of K. puncak is notably different from the other two species: it is tubercular dorsally and on the upper lateral flanks, while the lower flanks, chin, abdomen, and posterior sides of the thighs exhibit an areolate skin pattern.

Kalophrynus puncak hides in moss (image), under logs, or beneath leaf litter, from where males call during the day. The call is a single, short, pulsed note with a dominant frequency ranging from 1.75 to 2.52 kHz.

At the upper elevations of Gunung Mulu, this species is the most abundant amphibian but is difficult to find due to its small size and secretive lifestyle. Its diet consists of ants, termites, and other small arthropods. The larval stage remains mostly unknown, but Fukuyama et al. (2021) discovered a terrestrial clutch in moss at the base of a tree.