The Fly River roundleaf bat was described as a new species in 1886 by British mammalogist Oldfield Thomas and Italian naturalist Giacomo Doria.

The holotype had been collected by Luigi D'Albertis along the Fly River of Papua New Guinea.

[3] In 1963, however, John Edwards Hill included the Fly River roundleaf bat as part of the Hipposideros cyclops species group along with all previous members of the H. muscinus group, as well as H. cyclops and H.

It has been documented at a range of elevations from 0–750 m (0–2,461 ft) above sea level.

[1] As of 2017, the Fly River roundleaf bat is evaluated as a least-concern species by the IUCN—its lowest conservation priority.