The anti-cancer vaccine Gardasil will be free for all boys and girls, and access to a vaccine against chicken pox will be widened.
Pharmac has announced the decisions today.
The Gardasil vaccine has been available free for Year 8 girls but boys have been excluded because of the cost.
Pharmac has announced it will now fund the vaccine for all children and adults up to the age of 26 from next year.
It means boys will be included in the human papillomavirus (HPV) vaccination programme in schools.
The current four-strain vaccine will be replaced with one covering nine strains.
Pharmac director of operations Sarah Fitt said the organisation had been working on this and other changes announced today for a long time.
"It's a complicated package and in fact this isn't even all of it - there's actually still another six vaccines that are part of this package that we've been working on."
"So what we've been able to do is on some of the vaccines we've been able to get some quite good savings and then that then enables us to widen access in other areas and introduce new vaccines."
Kate Baddock, a Warkworth GP and chair of the Medical Association's General Practice Council, welcomed Pharmac's decisions.
"It's fantastic news, the MA's been lobbying for this since we started to get information that the rate of HPV-related cancers in boys and men were starting to increase.
"It will protect not only boys from HPV infection and related cancers but it will also protect girls and women."
Boys would be protected against cancers little known by the public.
"It's to protect against what they call ano-genital cancers. So cancers of the anal canal and cancers of the penis."
The fact boys were to be vaccinated would also protect girls, she said.
"If there are girls who are missing out on the vaccine, then there will be a greater herd immunity with boys also being done."
A chicken pox vaccine would also be added to the childhood immunisation schedule for the first time, at 15 months.
There would be a free catch-up dose at age 11 for previously unvaccinated children and those who had not had chickenpox.
Dr Baddock said the extension of the chicken pox vaccine was also a good decision to protect against what she called "a debilitating, miserable illness that can cause scarring".
Until now the chickenpox vaccine had only been funded for high-risk patients.
Immunisation Advisory Centre director of research Helen Petousis-Harris said it was fantastic news - and about time.
"Every year there are about 55,000 cases of chicken pox in New Zealand and 450 hospitalisation and that can include some admissions to intensive care and now we can help prevent it, which is great.
Dr Petousis-Harris says when other countries introduced the vaccine, chickenpox had largely disappeared.
Pharmac said the changes and others announced today would affect 100,000 people.