Biosecurity Queensland says the result was confirmed on Friday and the horse was euthanised after its condition deteriorated rapidly.
The Hendra case is Queensland's first since 2017.
Biosecurity Queensland has isolated the property as staff work to identify the source of the virus and ensure humans have not been exposed.
"Tracing and risk assessments have been undertaken on other animals on the property," Biosecurity Queensland chief veterinary officer Allison Crook said.
"We are working with the property and horse owners to ensure the risk is contained on the property."
The horse that tested positive had not been vaccinated against Hendra.
The virus was discovered in 1994 following an outbreak of illness in horses at a racing stable in the Brisbane suburb of Hendra.
It can spread from flying foxes to horses, horses to horses and rarely, from horses to people. It can be fatal in humans.
"Hendra virus infection can occur throughout the year so it's important that horse owners take steps to protect themselves and their animals at all times," Dr Crook said.
Horse owners are urged to seek advice if an animal shows any symptoms of the virus, including a rapid onset of fever, an increased heart rate and rapid deterioration with respiratory and/or neurological signs.
"If a horse becomes sick, owners should contact their veterinarian immediately," Dr Crook said.
"People in contact with horses need to remember to continue to practise good biosecurity and personal hygiene measures even if a horse is vaccinated against Hendra virus."
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