It is a very poorly known species. Some records of R. subrufus are from caves (M. Duya pers. comm., Heaney et al. 1998), and it is assumed to be associated with lowland tropical forest. They are locally common in karst areas, but infrequently encountered elsewhere (Heaney et al. 2016). 

The Small Rufous Horseshoe Bat (Rhinolophus subrufus) is endemic to the Philippines, where it has been recorded on Camiguin, Catanduanes, Leyte (Silago and Ormoc provinces), Luzon (Abra, Aurora, Benguet, Cagayan, Camerines Norte, Camarines Sur, Isabela, Laguna, Pampanga, Rizal, Quezon and Sorsogon provinces), Mindanao (Agusan Del Norte, Davao del Sur, Sarangani, and South Cotabato provinces), Mindoro, and Negros (Bacnotan, La Union and Murcia provinces) (Cabauatan et al. 2014, Heaney et al. 1998, 2016, M. Duya pers. comm., Warguez et al. 2013) islands. It has been recorded from near sea level to over 1,000 m Asl (Heaney et al. 1998).