South Australian children aged three and younger will receive free vaccinations against the potentially deadly meningococcal B disease under a new state government program.

The policy will provide immunisations for children aged up to 12 months as well as catch-up programs for children aged under four years and, later, adolescents.

"It currently costs parents up to $500 for a full vaccination course to immunise their children - a cost which is out of reach for many," Health Minister Stephen Wade said on Wednesday.

The vaccinations will be available from GP doctors from October 1 for infants and children, and from early 2019 for students in years 10 and 11, as well as young people aged between 17 and 20.

SA Health's chief medical officer, Professor Paddy Phillips, said the program targeted the people who were most at risk.

"We know that meningococcal B disease occurs more frequently in infants and children up to four years of age and young adults aged between 15 to 20 years of age," he said.

Prof Phillips said there has been 372 cases of meningococcal B in the state since 2000, with 60 per cent of those cases in people aged under 21.

Of the cases, 14 resulted in death.

"This program would prevent about 12 cases of meningococcal B disease each year, and prevent one death every two years, as well as reduce the amount of disability experienced by those who survive the disease," he said.