This species was named along with 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 type locality, at different elevational levels. The name K. puncak refers to the fact that this species endemic to the highest elevations at Gunung Mulu, specifically 2110-2376 m. At the lower end of the range, it overlaps with K. nubicola.

Kalophrynus puncak is a small Kalophrynus. Adult males measure 19.6 to 22.7 mm in snout-vent-length, females 24.8 mm. The species is slightly bigger than both K. nubicola and K. dringi. It lacks the yellow snout patches of K. nubicola; its blueish iris and lack of a dorsolateral stripes distinguishes it from K. dringi. Furhtermore, the skin of K. puncak is notably different from the other two species. It is tubercular dorsally and at the upper lateral flanks; lower flanks, chin, abdomen, and posterior sides of thighs show an areolate skin pattern.

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

At the upper elevations of Gunung Mulu, the species is the most abundant amphibian but difficult to find due to their small size and secretive lifestyle. The food consists of ants, termites and other small arthropods. Larval live is mostly unknown but Fukuyama et. al 2021 found a terrestrial clutch in mosses at the base of a tree.