The species' distribution in KwaZulu-Natal indicates a wide range of habitats from drier Valley bushveld and Lowveld to moister Mistbelt (including forest habitats), where suitable cover is present in the form of caves, overhangs, and unused mine and railway tunnels (Taylor, 1998). Roosts in caves, overhangs, disused mines, railway tunnels and similar habitats (Skinner and Chimimba 2005). In KwaZulu-Natal it has been found in damp sandstone caves, a solution cave of poorly consolidated glacio-fluvial boulder clay, a rocky overhang over a forest stream, a rock fissure, a railway tunnel as well as from unused mine adits (Taylor, 1998).

This species is present in Central Africa, East Africa and southern Africa. It is known from a number of discrete ranges, the largest of which stretches down south-eastern Africa, from Malawi, Mozambique and Zimbabwe, down to South Africa (where is extends along the south coast). It is also known from eastern Democratic Republic of Congo near the borders with Uganda and Rwanda (although this population needs to be confirmed as Miniopterus fraterculus), and recorded from localities in Tanzania, Zambia, and Kenya. A small recorded range in Kenya near the border with Tanzania probably does not represent Miniopterus fraterculus.

This species is presumably present in a number of protected areas. In Tanzania it is present in the Manga Forest Reserve of Tanzania (Doggert et al. 1999). Further studies are needed to better define the range of this species.