The first vaccinations followed three deaths in 1999
The second round of inoculation has started at Porth County Community School in the Rhondda, after two children at the school contracted the disease after having the vaccination two years ago.
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It is thought the vaccine used at schools across Rhondda Cynon Taff in 1999 was stored at too low a temperature, rendering it less effective.
The initial vaccination programme was prompted by a severe outbreak in south Wales, which led to three deaths and the declaration of a public health emergency.
On Monday, the first of 25,000 pupils received a second jab against meningitis C - a strain of the disease which causes an inflammation of the brain lining and can be fatal within hours.
The jabs - offered to those aged between seven and 18 - are due to be completed by mid February.
But some parents have criticised that staggered approach to the programme.
But they have been urged not to worry during the wait for the booster, as the initial vaccination offered some resistance to the disease.
The need for a second round of vaccinations is a blow to Bro Taf health officials, who have stressed the programme is a "precautionary" move."
A spokesman for the authority said the measure was a mark of its vigilance, and the Welsh Assembly said it was "not unusual" for children who have been vaccinated to contract the disease.
A spokesman for Bro Taf said: "Cost doesn't come into it - it's something that has to be done.
"It might not be the vaccine. There's very many factors behind why the number of antibodies might not be so high."
While there is an annual increase in the number of reported meningitis cases each winter but, at the time of the three deaths, cases of meningococcal meningitis leapt from 277 the previous year to 464.
A spokesman for the Welsh Assembly administration said it was "not unusual" for a few children who had been vaccinated to contract the disease.
He maintained that the re-vaccination was proof of the authority's vigilance.
Health officials added that approximately 95% of children nationally who are immunised will develop antibodies in their blood against meningitis C.
But children in the Rhondda Cynon Taff area are thought to have lower levels of resistance. A statement by the health authority read: "All children in that area who to date have received only one dose of the MCC vaccine will be offered a second booster dose of the vaccine.
Bro Taf said it is working closely with the UK National Joint Committee on Vaccination and Immunisation, the Public Health Laboratory Service and the National Assembly for Wales.