After an earlier attempt at surgery failed, Sebastian suffered a stroke.
Sebastian Selo, from south London, had a rare tumour-like tissue growth in the brain, which causes him to have dozens of epileptic fits every day.
His parents Louie and Anna Selo raised £25,000 to pay for the flight and medical treatment.
Sebastian had a hypothalamic hamartoma (HH), which is a ball of tissue the size of a grape in what should be an empty cavity.
The Royal Children's Hospital in Melbourne, where the operation was carried out, leads the field in carrying out the procedure.
His parents told the BBC they had to make a hard choice about whether to go ahead with the operation.
Seizures
Sebastian's father Louie said: "We know its high risk, but we have to give him something."
His mother Anna added that if the operation succeeded: "It would seem like a miracle, performed by the 'Wizard of Oz'."
After an earlier attempt at surgery failed, Sebastian suffered a stroke.
Sebastian flew to Australia for the operation 12 days ago.
The team, led by Professor Jeffrey Rosenfeld, began the operation, which lasted between five and six hours, at 0415 GMT on Tuesday.
A spokeswoman for the hospital said: "Doctors say there is a 50-70% chance that Sebastian will be completely seizure-free."
Sound waves
Dr Simon Harvey, from the Royal Children's Hospital's epilepsy program, said the tumour would be sucked out with an "ultra sonic aspirator", which uses high frequency sound-waves to break down the tissue ball.
He said Sebastian was starting to come round from the operation and was starting the move the side that had not been affected by his stroke.
Sebastian was born with HH, which also affects his appetite, emotions and behaviour.
He is also unable to speak and walks with a limp because of his condition.
During the operation, doctors made incisions from the top of the brain instead of the base, to avoid nerves and arteries, and to lessen the danger of a stroke occurring.
Children have flown to Australia from all over the world for the procedure, which has been performed 18 times over the last four years.
Eleven of them are now completely free of seizures, five improved "dramatically", and two showed moderate improvement
Sebastian will stay in Melbourne for a month for observation and further tests after the operation.