Kalophrynus punctatus was described as early as 1871 by Peters, with the type locality given simply as "Sarawak." However, the original description is brief and lacks detail. Inger (1966) examined the holotype specimen as well as another specimen he discovered in the Rijksmuseum Leiden collection, labeled with the locality "Semedum." Zug (2015) summarized the available information on this species. Here, we draw from Zug’s account but emphasize that little is actually known about K. punctatus, including its distribution and variability. Distinguishing this species from other Kalophrynus can be challenging.

Males reach 23–27 mm in snout–vent length (SVL). The eardrum is visible but partly obscured by skin and is smaller than the eye. Fingers are unwebbed, with the length order 3 > 2 ≈ 1 > 4; toes are lightly webbed, with the length order 4 > 3 ≈ 5 > 2 > 1. The inner metatarsal tubercle of the foot is rounded, while the outer tubercle is absent.

In preserved specimens, the dorsal coloration is reddish brown, while the sides of the head and body are darker brown. Small black spots on the back may be present or absent. The underside has been reported as either dusky with light spots or pale yellowish white with a dark band under the jaw and smaller dark spots posteriorly. These color descriptions from the literature are of limited use for identifying living, unpreserved specimens.

In the future, it may be possible to extract DNA from the type material, allowing confident linkage of the types to living populations.