The Moderna vaccine will be used in the rollout that begins on Monday.
Health Secretary James Fong said the Moderna vaccine would be rolled out by school clusters across the country.
Dr Fong said unlike the workforce, vaccination for children would only be conducted with the consent of parents or guardians.
Parents and guardians will need to sign a consent form for their children to receive the vaccine, he said.
He said parents could register their child online through the Vaccine Registry Portal which is available from this weekend.
"Schools that are close to each other will be grouped together to form a cluster and where there's student rolls 15 to 17 years old can be vaccinated.
"The dates, clusters and venues of these schools will be announced this weekend for the roll-out to begin on Monday 20th, September."
Children will need to receive two doses of the vaccine at an interval of 28 days, Dr Fong said.
According to the Education Ministry, 26 percent of students over 18 years are fully vaccinated while 30 percent have only had their first jab.
Of the 9115 students in Year 13, 8349 students were over 18 years and the remaining 766 students were 17 years old.
Schools have been closed since April and Dr Fong said the safest and most sustainable way to get children back into the classrooms and to keep them there was vaccines.
He said the Education Ministry had advised their health counterparts that Years 12 and 13 students need to sit for their external exams to progress into higher education.
"We have decided to vaccinate children aged 15 to 17 years old first as these children are mostly in secondary school and some of them are nearing the end of their secondary education."
Dr Fong said while it was not mandatory for children to be vaccinated, he encouraged parents to get their children protected against the virus.
The vaccination details for children in the 12 to 14 age group will be announced later, he said.
"Children in this age category will receive the Pfizer vaccine but we will use the same approach as the Moderna."