Queensland has recorded 20 cases of the potentially deadly disease this year after 26 cases were recorded in 2022.
The jabs will be offered to newborns and children under two and adolescents aged 15 to 19 from 2024.
The Meningococcal B vaccine rollout will cost more than $90 million over three years, health minister Shannon Fentiman revealed before estimates hearings on Friday.
The vaccinations will be made part of the routine childhood and school immunisation programs and part of the state's largest state-funded rollout immunisation program.
It will be available through GPs, community vaccination clinics, and Aboriginal and Torres Strait Islander Health Services.
For secondary school students in Year 10, the meningococcal B vaccine will form part of Queensland's School Immunisation Program.
"This announcement is the single biggest investment in a state-funded vaccination program to date," the minister said.
"We know the meningococcal B strain can be lethal and – if a young person is lucky enough to survive the disease - it's likely they will develop permanent and sometimes devastating complications."
The vaccine is currently available to Queenslanders at around $100.
It is accessible under the National Immunisation Program for Aboriginal and Torres Strait Islander infants and all people with medical risk factors for invasive meningococcal disease.
"Our Queensland Meningococcal B Immunisation Program will remove the financial barriers to vaccination and ensure those who need it most can access it.
"Almost half a million infants, children and adolescents will be eligible to receive the MenB vaccine from quarter one 2024."
Queensland Chief Health Officer John Gerrard said the MenB strain has emerged as the most common cause of illness and death of the disease.
"It's important to note that while invasive meningococcal disease is rare, it can be very dangerous," Dr Gerrard said.
"We regularly monitor trends of strains causing invasive meningococcal disease and will continue to do so."
Symptoms of the disease include severe, unexplained limb pain, difficulty waking up, high-pitched crying in babies, severe headache, aversion to bright lights, stiff neck and a red-purple rash that doesn't disappear when pressed with a glass.
The rash does not always occur or may present late in the illness.
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