"There are 700 million people on our continent with 565 neurosurgeons, that is one surgeon per 1.2 million people," said retired Archbishop Desmond Tutu who opened the conference.
In Africa poor diet and peri-natal care means higher incidences of treatable conditions - such as water on the brain, spina bifida and tuberculous meningitis - than anywhere in the first world.
"Something basic like the treatment and management of hydrocephalus (water on the brain) is very different in Africa because of the cost of the treatment and the expertise needed," said William Harkness of Britain, who is on the board of the International Society for Paediatric Neurosurgery.
Abat Sahlu, a resident neurosurgeon in Ethiopia, told AFP there were only four neurosurgeons serving 80 million people in his country.
"In one hospital we have 400 paediatric patients waiting for surgery. They wait up to four years," he said, adding many would die awaiting treatment.
Zambia has two neurosurgeons for 11 million people. The Ivory Coast has 10 specialists serving 20 million residents and people from countries such as Liberia and Sierra Leone who have none.
Tony Figaji of the Red Cross children's hospital in Cape Town - the only specialised unit in sub-Saharan Africa - said brain tumours were the second most common malignancy in children after leukemia.
"For a child who has a brain tumour the primary thing making a difference to whether they will survive is to have an operation," he said.
Head injuries were the leading cause worldwide of death in children over four, and in South Africa there was up to a seven times greater chance of a child dying from a head trauma, Figaji said.
The conference, held for the first time in sub-Saharan Africa, includes training for neurosurgeons around the continent.