Queensland chief veterinary officer Dr Rick Symons said the animal was euthanised last Tuesday after returning a positive test for the bat-borne virus.
It was one of the two remaining horses at the property, where a horse had been euthanised the Tuesday before.
"Samples were taken for Hendra virus testing from the two horses remaining on the property and we received a positive result for one of these horses," Symons said.
"Three horses have now died at this property in the past fortnight.
"One was euthanased almost two weeks ago after becoming seriously ill and being diagnosed as suffering from colic.
"No samples from that horse are available for testing and we will not be able to confirm if that horse was actually infected by Hendra virus."
Symons said the property would remain under quarantine until at least late November.
The Hendra virus incident is the 10th in Queensland this year and this latest case is the 13th horse to be infected with the virus. Ten horses have died in outbreaks in New South Wales.