There have been 1,100 confirmed cases of pertussis in the province.
About 40 per cent of the cases have been reported in Moncton, with another 11 per cent in Fredericton.
Chief medical officer Dr. Eilish Cleary says the majority of cases are among children between the ages of 10 and 14.
The immunization program will begin this fall with public health nurses visiting schools and clinics established.
The highly contagious disease is easily spread through droplets from the nose, mouth and throat.