After failing to secure NHS funding, professor Steven Gill now hopes to raise £900,000.
Some 18 children with diffuse intrinsic pontine glioma brain tumours would be treated at the Bristol Royal Hospital for Children in the clinical trials.
Professor Gill said he understood the NHS was "not a bottomless pit."
"There are many treatments where you have to be really highly selective and say you're better of doing five hips, rather than one very expensive operation on somebody who has got very little chance of surviving," the Southmead Hospital neurosurgeon added.
"These cruel decisions have got to be made.
"In this particular disorder, nothing that people have done has made any difference at all [including] chemotherapy [and] radiotherapy.
"On the other hand, if we can crack this one - which is the hardest type of tumour to treat - that spins out into treating a whole range of other different things."
Professor Gill said doctors have traditionally struggled to effectively deliver drugs through the blood-brain barrier to the area of the brain where they will be most effective.
He and his team at the University of Bristol and North Bristol NHS Trust use a "revolutionary micro-catheter system" to inject drugs directly to the brain.
He said the process could eventually offer hope to other neurological conditions including Alzheimer's and Parkinson's Disease.
Chief executive of the Funding Neuro appeal, which has helped launch the crowd-funding initiative, Sharon Kane, said the trial needed to be up and running "as quickly as possible".
"One minute a child is absolutely fine. Then they get diagnosed with this condition and the parents are told their child has nine months to live, and there's nothing you can do about it," she added.
A neurosurgeon from Bristol who has developed a "revolutionary treatment" for brain disease has launched a crowd-funding appeal to pay for trials.