The specific name naeyakai refers to the "naeyaka", spirits of deceased relatives in the believes of Vedda people living in the type locality area.

[2] Nannophrys naeyakai is associated with seasonal streams with rock crevices on hillsides at elevations between 200–620 m (660–2,030 ft) above sea level.

Vegetation consists of scattered trees, and there is a ground cover of grasses dominated by Cymbopogon species.

[1] This species is quite common at its two known locations, but searches at other hilltops in eastern Sri Lanka have not revealed new populations.

Threats to its habitat include changing land use practices (i.e., burning of the grassland, felling of trees) that reduce water retention and eventually impact the small streams that this species depend on.