About 150,000 children aged between two and five and around 400,000 primary school pupils will be eligible for the nasal spray vaccinations. The childhood flu programme will eventually be rolled out to cover all children aged from two to 17.
With children two to three times more likely to fall ill with flu than adults, it is estimated the programme could prevent an additional 200 deaths a year and up to 1,100 hospitalisations.
Dr Nicola Steedman, the Scottish Government's senior medical officer, said: "Flu can be very unpleasant for children, and in some cases it can develop into more serious health complications such as bronchitis, pneumonia and middle ear infection.
"Parents can make sure their child is safeguarded against flu by taking up the offer of this free vaccine.
"I'd encourage parents of primary school children to look out for the information on the flu vaccine when it comes home in school bags and to return the consent form as soon as possible.
"Parents of children aged between two and five should make an appointment with their GP from October."
Health Secretary Alex Neil said the programme's scale was "unprecedented".