"We're in this situation where we've had this hearing without [the boy's] view. He's not best placed now to have a view, is that right," he asked the father's lawyer.
She said the boy could offer views on receiving treatment which was being administered by a health worker at home under agreement with the boy's parents.
But she said the boy had yet to reach the age bracket of 10-12 years at which medical professionals believed children could be told they carried the virus.
She said there would be other events over the period of a possible order which could also require a return to court, including a study due for publication in 2016 which could have findings supporting the father's view.
The health board brought the case to court after years of trying to have him provide antiretroviral treatment to his son.
The father's lawyer said, summarising the man's position, said her client didn't accept the diagnosis for HIV and was concerned about side effects of the medication used to treat it - views which he believed were in his son's best interests.
She said her client had firmly held views after spending thousands of hours of researching HIV although mainly in areas outside mainstream medical thinking.
"It's not that he's not willing [to give the boy treatment]. He can't." She said the boy's father believed the medicine used to treat HIV was "highly poisonous".
She said his behaviour in maintaining positive relationships with clinicians while believing the medication they had prescribed was deadly had been "extraordinary and impressive".
The father had shown similar restraint and willing in coming to an informal agreement with the health board to allow treatment while the case was being decided in court, she said.
The lawyer said the lack of publication of her name - due to suppression orders - had led some to question whether she had difficulty being seen to act for the father.
She said she had completely such assertions. "It's been a privilege to represent my client. He ... cares very deeply about his child."
The lawyer for the health board said boy's awareness of his condition could impact on the case in the future. It could be he sided with his father's views on HIV - or with the clinicians who were treating him.
He said there was no realistic prospect of the father's views changing. "He can't contemplate he could be wrong and [the boy] would suffer adverse consequences if that was the case."
He said evidence showed the onset of a deadly illness could have quickly, rather than a gradual sickness.
He pointed to evidence from an HIV specialist which suggested the boy had a 9 per cent chance of developing Aids in the next year and a 2-3 per cent chance of dying as a result.