"It is the precise genetic targeting of the particular cancers in the particular patient that enables (it) to make sure the treatment is the key."
Australia's eight children's hospitals will be a part of the program, bringing together research to identify personalised therapies for patients.
Every child with high-risk brain cancer, at diagnosis or relapse, will have their tumour undergo extensive genetic profiling and their tumour cells will be analysed to determine a response to anti-cancer drugs.
The $5 million will also allow for the staffing and research into developing routine immuno-profiling methods.
Two-and-a-half-year-old Kristian Kozul from Melbourne was diagnosed with an aggressive brain tumour at just 15-months-old.
He underwent five rounds of chemotherapy but the tumour continued to grow.
The youngster became a part of the trial when tests revealed a rare genetic mutation and the Kozuls' temporarily moved to Sydney for the new treatment.
He is now given liquid medication by his parents twice a day and mum Marie said the change of therapy has had a profound difference.
"Since he's been on it, (the tumour's) been stable, it hasn't continued to grow," Ms Kozul told reporters.
"(The treatment's) not as invasive as chemo so he's tolerating it a lot better, he's presenting a lot better he's growing, his development's changed significantly."
Zero Childhood Cancer started with a pilot study in late 2015 by the Children's Cancer Institute in Sydney and the Kids Cancer Centre at Sydney Children's Hospital.