Limnonectes nephophilus is a montane species with known records from 1200 m to >2000 m a.s.l. At Gunung Mulu the species overlaps with the sympatric L. gunungensis at its lower elevation range. Type locality is Gunung Mulu, Camp 3. Apart from Mulu National Park, current records also identified the species at Pulong Tau National Park (Gunung Murud).

Limnonectes nephophilus exhibits the typical characteristics of the palavanensis-species group. These include a small body size (snout–vent length less than 40 mm), low and inconspicuous odontoid processes on the lower jaw in both males and females, and a finely shagreened dorsal surface with prominent longitudinal dorsolateral glandular ridges. The interorbital distance is equal to or greater than the width of the upper eyelid. The toes are not fully webbed, and a horseshoe-shaped dermal ridge is present in the middle of the dorsum, just behind the point where the forelimbs insert.

This species differs the other members of the palavanensis-species group by a combination of features: the toe webbing is very reduced; the supratympanic fold is subangular, with the front portion shorter than the rear; a clearly visible pineal spot is located slightly anterior to the level of the front edge of the upper eyelids; vomerine ridges are short and widely spaced; and a low, indistinct median ridge runs from the nostril level to the pelvic region. Unlike some related species, it lacks postpalpebral and lumbar ridges.

The coloration is brownish above sometimes with reddish or orange tints. The ventral side of the head, chest, arms and lower legs are yellowish cream-white. Large dark brown spots iare present n infralabial region. The throat is speckled with minute brown dots. The abdomen is hardly pigmented, appearing blueish white. The thighs are reddish cream-coloured.

It is considered relatively large for the group, adult males measure between 26 and 32 mm in SVL, and adult females between 33 and 38 mm. 

The advertisement call has been described by Dehling et al. (2025) as a series of up to 21 sharp chirps over a duration of approx. 5.5 s.