Jonathan Simms, 18, from Belfast, will now be given repeated infusions of the drug pentosan polysulphate directly into his brain.
The intial procedure is reported to have gone smoothly.
Jonathan's father, Don, and the family of another teenage vCJD patient took an NHS trust to court to get the treatment approved.
"
It's an experimental treatment but it's not experiment for experiment's sake
"
Don Simms
While laboratory experiments suggest it has the potential to tackle the condition, the drug is controversial because it has only received limited testing in animals.
The location of the hospital treating Jonathan, the identity of the second patient, and the names of the surgical team involved cannot be published for legal reasons.
Brain tube
In a simple procedure, a tube has been inserted into his brain so that the first infusion can be given.
It is hoped that eventually, a total of 12 infusions, with gradually increasing doses, can be given.
It is likely to be some time before the impact of the treatment can be fully assessed.
However, fears remain that it may cause harm - and perhaps even hasten the death of the two patients.
Don Simms told the BBC that while he was concerned about the treatment, it was Jonathan's only chance.
He said: "We're relieved to some degree that we are here, but at the same time we are quite frightened because we are stepping into the unknown."
Jonathan's progress will be monitored using regular scans checking for the presence of bleeding around the injection site.
Slowing hope
Jonathan's condition has deteriorated in the months that his father has been campaigning for him to have the drug.
He now requires round-the-clock care and the disease has severely affected his speech and eyesight.
Mr Simms said there was still real hope that the drug might be able to slow the rate of progress of his son's illness - or perhaps even clear the "rogue" proteins that cause it from his brain.
He said: "I don't like the word 'guinea pig'.
"It's an experimental treatment but it's not experiment for experiment's sake."
Permission for the drug to be used was given after a hearing at the High Court.
However, the NHS trust at the centre of the case continued to refuse to allow the treatment to be carried out there even after Dame Elizabeth Butler-Sloss delivered her ruling in favour of the families.
In the ruling, she said: "Where there is no alternative treatment available and the disease is progressive and fatal, it seems to me to be reasonable to consider experimental treatment."
The Department of Health has been working behind the scenes to find an alternative venue for the operations to be carried out.
Don Simms told the BBC: "Along the way we have become very weary - we are now battle-hardened.
"But there was never any time we wanted to give up."
More than 100 people in the UK are known to have died from the variant form of CJD so far, with a handful now living with the illness.