Children from 9 months to 5 years old and teens from 13 to 19 would be given the first vaccines to be available.
They would be administered at Northland-wide clinics at schools and community centres, starting this week.
The DHB said it hoped even parents opposed to immunisations would have their children vaccinated against the fast acting, atypical symptom and lethal MenW.
Through Pharmac, the Northland DHB was able to source only 20,000 doses as there is a world-wide shortage of the vaccination due to the rise of the MenW internationally.
The two qualifying age groups have been chosen because of their vulnerability and because those two groups have more potential to spread the bacteria through saliva, respiratory droplets and close body contact.
''The only effective way to manage this outbreak is with a vaccine programme,'' DHB chief executive Dr Nick Chamberlain said.
The DHB is trying to procure another round of doses so the middle children's age group can be vaccinated early next year.
''We know there's going to be significant anxiety among parents of that group,'' DHB paediatrician Ailsa Tuck said.
Even if they have no symptoms, carriers can infect those around them. Vaccinating the two age groups would lower the number of carriers in Northland and stop the spread of meningococcal disease across the entire community, she said.
Meanwhile to also lower the spread, people should cover their nose or mouth when sneezing or coughing, then wash and dry hands afterwards.
They should also avoid sharing eating or drinking utensils, toothbrushes and pacifiers.
