Roberts, originally from Auckland but now residing in Devon, wanted a second operation to be delayed until more doctors had been consulted.
However Bodey agreed with specialists that follow-up surgery to remove a 1.5cm residual tumour needed to be carried out urgently.
A doctor treating Neon told the judge on Thursday the seven-hour operation went well.
Despite wanting the second operation delayed, Roberts said her son is in "amazing spirits" following the operation, the Daily Mail reported.
"His sense of humour is amazing. He is doing so much better than he was after the first operation."
However the court was told Roberts is still refusing to let doctors give Neon anti-sickness drugs.
Roberts told the court earlier this week she is not a "bonkers mother".
She fears radiotherapy will reduce Neon's intelligence quotient (IQ), shorten his life, put him at risk of having strokes and make him infertile.
Roberts has said she would agree to Neon being given chemotherapy because any damage caused could be "overcome".
"The mother remains concerned that radiotherapy is not in Neon's best interests," Ian Peddie QC, for Roberts, told the judge.
"We assert that there are doctors who can offer credible alternative treatment to the therapy that is proposed."
Neon's father Ben, who lives in London and is separated from Roberts, has agreed to radiotherapy but is "apprehensive", the court has heard.
A specialist treating Neon has described Roberts' comments as "sensible" and accepted that there could be side-effects to radiotherapy.
But he said without radiotherapy the little boy could die within a few months.
And Victoria Butler-Cole, who is representing doctors involved in Neon's care, told the judge that Roberts was proposing "experimental therapies", which are "unproven", as alternatives to radiotherapy.
Roberts, 37, ran away with her son earlier this month in the midst of a legal battle over whether the boy should undergo radiation treatment following surgery in October to remove a brain tumour.
The pair were found five days later following a nationwide search.
- AFP with nzherald.co.nz
