A meningococcal catch-up programme is set to be funded for people aged 13 to 25 in their first year of close-living situations.
PHARMAC deputy medical director Dr Pete Murray said about 35,000 people living in boarding school hostels, tertiary education halls of residence, military barracks and prisons would be able to get the vaccine.
It was estimated about 8000 additional people per year would get the vaccine.
Associate Health Minister Julie Anne Genter called meningococcal, which can develop into meningitis or septicaemia and have long term consequences, a "serious threat which people at higher risk should be protected from".
"Cases of meningococcal are still relatively rare, but the consequences can be extremely serious, even fatal, and we know young people in close living conditions are at greater risk."
"New Zealand sees a number of meningococcal cases in our young people every year. The latest figures show 120 cases in 2019 to date, sadly with eight deaths. Around half of these cases were in the W, C and Y strains."
The roll out will begin on December 1 - with young people living in close situations already eligible for one dose.