For the first time, all children will have the chance to be protected from the disease.
Previously, only those youngsters who were classed as being in one of the at-risk groups - such as young carers or children with conditions such as asthma - would have been offered this.
The vaccinations are being phased in from this autumn and will be rolled out over the next two years.
The first phase will see all children aged two to three offered the vaccine this year, as well as children from a number of primary schools in every health board area.
About 120,000 two and three-year-olds and about 100,000 primary school pupils will be offered the vaccination - which is given using a nasal spray - over the 2013-14 flu season.
By towards the end of 2015, about one million children aged between two and 17 will have had the chance to be immunised.
The programme is being brought in following advice from the Joint Committee on Vaccination and Immunisation - an independent, expert committee which advises UK health departments.
The nasal spray is being used because it provides children with better protection from the flu than the previous vaccine injections
Scotland's top doctor, Chief Medical Officer Sir Harry Burns, said: "Flu is a serious illness and the extension of the flu vaccination programme will protect those children who receive the vaccine and will help to protect against the spread of flu."
He added: "The vaccine offers excellent protection against those types of flu virus that are most likely to be circulating each winter, protecting your child from a nasty illness that could end up with them having treatment in hospital.
"The immunisation is safe, quick and painless, and has been used in a number of other countries, including the US, for many years."
As well as the new vaccination programme for children, the regular flu vaccination programme will continue for those with underlying medical conditions, those aged 65 and over, pregnant women, health and social care workers and unpaid careers, including young carers.
Sir Harry said: "In addition, it is important that those people who are in the clinical at-risk groups for flu immunisation continue to be vaccinated to protect themselves against the virus."