Biosecurity Queensland said the case occurred on a property outside Bowen.
Deputy chief veterinary officer Rick Symons said a veterinarian had reported a suspect case to Biosecurity Queensland last week after attending a sick horse on the property.
"The vet attended the horse over several days last week and samples were taken and forwarded to Brisbane for testing. The horse was euthanized on Thursday," Symons said.
"The sample results came back last night as positive and we immediately began implementing control procedures.
"There is one other horse on the property, which is healthy. A third horse on the same property died one month ago but we do not have any samples to test," he said.
"The property is under quarantine.
"There is one resident at the property who has been informed of the test results.
"There are a number of horses on an adjoining property and Biosecurity Queensland officers are working with the owner to assess what, if any, exposure there has been to the most-recently deceased horse.
"Staff will also speak to a small number of residents in the immediate area today and provide the latest information about Hendra virus."
The case is the 13th known incident of Hendra virus infection in horses since 1994.
The case follows an outbreak near Rockhampton, at Cawarral, in August, which resulted in the death early in September of veterinarian Dr Alister Rodgers.
Hendra is able to be transmitted from horses to humans through contact with body fluids. Dr Rodgers was the fourth person to have died from the infection, among the seven known cases among people.