Hendra virus (HeV) can cause potentially fatal respiratory and neurological disease in horses and humans. Australian flying-foxes (genus Pteropus) are the natural reservoir host for HeV. There is limited understanding of the route of transmission for the spillover of HeV from flying-foxes to horses and also for the route of transmission for the enzootic maintenance of HeV within flying-foxes; although exposure to flying-fox fluids (i.e. urine) contaminated with HeV is hypothesised to play a role. Flying-foxes also host blood feeding ectoparasites know as bat flies (genus Cyclopodia). Whilst there are no examples of paramyxoviruses that utilise insect vectors for transmission, there has been limited investigation of these haematophagus insects as potential vectors of HeV. A total of 186 bat flies were collected from flying-foxes (Pteropus alecto, P. poliocephalus and P. scapulatus) between December 2013 and June 2014, when the average prevalence of HeV in the flying-fox roost was 3%. Bat flies were sexed and then dissected to expose the internal organs with specific attention to the crop, gut and when available, the larvae. RNA from dissected tissues and larvae was extracted using the MagMAX Viral RNA Isolation Kit and tested for HeV using a qRT-PCR targeting the M gene. All bat flies and larvae from this study tested negative for HeV. The probability of failure to detect HeV in these bat flies at a prevalence of at least 3% was <0.004. 0>This study provides the first molecular based evidence that bat flies are unlikely to be a transmission vector for HeV between flying-foxes and in spillover events. This study also demonstrated the utility of studying a potential vector in tandem with the natural reservoir host to allow appropriate interpretation of results.