Around three-quarters of youngsters diagnosed survive for at least five years thanks to advances.
But the effects of radiotherapy mean two-thirds suffer long-term side effects, including learning disabilities and hormone deficiencies.
The funding will help scientists who are creating an "atlas" of young patients' brains to map out where the most damage occurs during radiotherapy and to understand how to make treatments kinder.
Paediatric junior doctor Josh Goddard, 32, was diagnosed with spinal cancer aged 12 and had radiotherapy to his head and spine, plus chemotherapy.
The radiotherapy led to cancer in his thyroid, a gland in the neck that secretes growth hormones, which had to be removed. Josh now needs daily injections of human growth hormone and levothyroxine tablets.
He said: "It's incredibly important that we find treatments that don't cause long-term side-effects.
"I've found my brain processing power isn't as quick as it used to be.
I have a reduction in energy levels and I don't think my short-term memory is as good." Other side-effects include skin on his head that is particularly sensitive to sunlight. Josh added: "When I was told I was going to have radiother apy, I remember my dad saying he felt like it was archaic.
"We don't know whether the radiotherapy was effective because we did both at the same time. But my dad still wishes I never had radio therapy."
The medic, from Lancaster, has an inoperable seven-inch tumour at the base of his spine. It causes him some pain and numbness in his legs but has remained stable for around a decade.
Some 400 children in the UK are diagnosed with brain tumours each year.
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