It comes after the Joint Committee on Vaccination and Immunisation concluded that the benefits of vaccination of this group outweigh any risks, but that no UK-wide recommendation would be given.
It was left to Chief Medical Officers to consider the issue, and they have decided in favour of vaccination.
Vaccines will be offered to 12-15 year olds from Monday September 20, Nicola Sturgeon said in an update to the Scottish Parliament on Tuesday.
"We believe that vaccination of 12 - 15 year olds is important and we will therefore move to implement the advice as quickly as possible,” she said.
"It is, of course, important to stress the importance of informed consent. I know that many young people and their parents will have questions.
"Material will be made available online later this week. It will be appropriate to both young people and adults. It will seek to answer questions and provide balanced information to help young people and their parents
make informed choices.
"And I can confirm that from Monday 20 September, so Monday coming, drop in clinics will be open for any 12 - 15 year old who has read the information and - in discussion with parents and carers - decided they wish to be vaccinated.
"It will of course be appropriate for parents or carers to accompany their children to clinics, and vaccinators will be on hand to answer any further questions or address any concerns.”