The children of Ironville will be given the Group C Conjugate Meningoccal Vaccine following the third outbreak of the disease in the village in the past two years.
It is understood a four-year-old girl has just recovered from the disease, while an eight-year-old boy is being treated in nearby Nottingham's Queen's Medical Centre.
Southern Derbyshire Health Authority requested special permission to use the vaccine from the head of the county's vaccination programme.
Speaking at the Ironville and Codnor School, scene of previous vaccination programmes, Dr Roy Fey, a communicable diseases consultant, said: "These are exceptional circumstances ... It appears there is more of a problem here than anywhere else in the country - we have vaccinated before but it just keeps coming back."
He said previous vaccines had saved lives, but the new one was expected to be much more effective.
The disease has traumatised the village over the past two years, with the death of one four year-old boy, Luke Pryor, and five other confirmed cases.
Mothers in the village of around 1,600 people are becoming expert in looking for signs of the bug.
Julie Worton, a mother of three, said: "Now I am checking my kids all through the night to make sure they don't have the symptoms."
Other mothers in the village, yesterday queuing with their children outside the school, said they were happy something was being done, but sceptical it would make any difference.