A court has ordered a six-year-old boy undergo cancer treatment for a malignant brain tumour despite his parents wishes.

A Perth court has ordered a six-year-old boy undergo chemotherapy for a malignant brain tumour after his parents had refused treatment.

A Princess Margaret Hospital doctor took legal action after the boy's parents argued they could not bear to see their son suffer the side effects of cancer treatment, the West Australian and Seven News said.

"I have watched and learned what all these children and their families go through and it is nothing short of toxic hell," the mother argued.

"The children are not really alive, they are completely drugged and exhausted and on the verge of death."

But WA's Family Court has ruled he should start treatment after his birthday party on Sunday.

The court was told the boy had a 30 per cent prospect of surviving for five years if chemotherapy started immediately and a 50 per cent chance with both chemotherapy and radiotherapy, but could die within months without it.