Nepenthes burbidgeae is probably the rarest of the Nepenthes species native to Mount Kinabalu. Its typical habitat consists of mossy forest or montane forest, where it often grows in low scrub and exposed areas on the tops of steep ridges. The species is restricted to ultramafic soils. In more exposed areas, N. burbidgeae is often found climbing amongst bushes of Leptospermum javanicum. At some localities it has also been recorded from bamboo forest.