The meningitis ACWY vaccine is to be offered in all Hampshire secondary schools from January 2018.
Currently the jab is offered through GP surgeries in the south of the county and school nurses in the north.
NHS England said there was "strong evidence that providing immunisation in schools increases uptake".
Hampshire is among 19 out of 152 English local authority areas where not all children are vaccinated through schools.
Six areas offer the vaccine through GP practices, while 13 have a mixed school and GP delivery model, according to the latest data for 2015/16.
The Men ACWY vaccine was introduced in August 2015, replacing the Men C jab.
It followed "a rapid rise in a new and particularly deadly strain of meningococcal meningitis and septicaemia (Men W)", the Meningitis Research Foundation said.
Head of research Linda Glennie said: "It's good news that the NHS in Wessex will now offer adolescent vaccines through schools.
"Uptake of Men ACWY vaccine via the school route has been as high as 84% in some areas. Unfortunately, uptake among older teenagers who were offered it free from their GP has been worryingly low - only 33% of school leavers in 2016 had taken up the vaccine."
- Meningitis is an infection of the meninges - the membranes that surround the brain and spinal cord
- Meningococcal bacteria are common and carried harmlessly in the nose or throat by about one in 10 people
- They are passed on through close contact
- Symptoms can include a fever, tiredness, and general aches at first. These can get rapidly worse, with agitation, confusion, vomiting and headaches
- People should seek help as soon as possible and should not wait for a rash to appear before getting advice
In a statement, NHS England Wessex said it had decided to change its delivery programme to improve take-up rates.
The government said the number of children vaccinated in Hampshire was unknown "due to technical difficulties in extracting data".
Meningitis W infection is fatal in one in 10 cases and can lead to long-term health problems including deafness, epilepsy and amputations.
Public Health England has urged young people going to college or university to be vaccinated, because their risk of contracting the disease is higher.