Harpyionycteris whiteheadi occurs in lowland and montane forest, in primary, lightly disturbed and secondary habitats. It has been found in an old reforestation area planted with exotic species but adjacent to secondary lowland forest, lowland and in montane forest. (Fidelino et al. 2020). These are fairly large bats that fly moderately high and are known to roost in trees, but not caves. They might depend on the fruits of viney pandans (Freycinetia spp.) (Heaney 1984, Heaney et al. 1989, Heideman and Heaney 1989, Rickart et al. 1993).

Harpyionycteris whiteheadi is endemic to the Philippines, where it is widespread excluding the Palawan Faunal Region and the Batanes/Babuyan group of islands. It has been recorded from Biliran, Camiguin, Cebu, Leyte, Luzon (Camarines Sur, there are no records from northern Luzon (L. Heaney pers. comm. 2006)), Maripipi, Masbate, Mindanao (Agusan del Norte, Bukidnon, Davao Oriental, Lanao del Norte, Lanao del Sur, Misamis Occidental, Misamis Oriental, Southern Cotabato, Suriago del Sur and Zamboanga del Norte provinces), Mindoro Oriental (Mt. Masulong, Roxas (Ong et al. 2013), Anahawin, River Calintaan (Gonzales and Dans 1995), Negros, and Samar. Its elevation range is from sea level to 1,800 m.

This species occurs in some protected areas (Mt. Apo Natural Park, Mt. Kanlaon Natural Park). Additional research is needed on the species distribution, population status and trends, and threats.