More than 300 schools in the greater Glasgow area are taking part in the scheme, together with all GP surgeries who will immunise children from the ages of two to five.
An awareness drive was launched yesterday before vaccinations begin on October 1.
The mass immunisation - which was piloted last year -aims to protect all children from two to 17 in the UK, to prevent 200 deaths and around 1100 hospitalisations.
Jennifer Reid, immunisation co-ordinator for NHS Greater Glasgow and Clyde, said last year's winter flu programme had a 65% take up rate.
Health chiefs hope to boost that further this year, she said. Nationally, it was 67.2%.
Ms Reid said: "We've got 334 schools taking part, with 98,000 children.
"I think because last year was the pilot it might have put some people off. It's important people realise it wasn't a pilot of the vaccine, but of the way it is delivered.
"It's a very large scale programme and we were testing whether it would work last year.
"Some areas immunised from primaries six and seven. Greater Glasgow and Clyde did all primaries."
She said an alternative vaccine was available for those who didn't want their children to get the nasal spray, which contains traces of a pork gelatine, on religious grounds.
It is also available for those with immune deficiencies who may not be suitable for the spray.
Consent letters are being sent to parents from schools this week.
Immunisation will take place from October until December 2.
Dr Nicola Steedman, senior medical officer for the Scottish Government, launched the programme which last year saw 130,000 children in Scotland vaccinated.
She said: "Flu can be very unpleasant for children, and in some cases can develop into 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.
"Parents of children aged between two and five should make an appointment with their GP from October."
Health Secretary Alex Neil said: "The scale of this vaccination programme, once fully implemented, is unprecedented.
"Immunisation is the best way of protecting against serious diseases, and the childhood flu programme is about ensuring more people than ever in Scotland are protected from the flu virus.
"Flu can hit children hard and even healthy children can become seriously ill, which is why we're offering the flu vaccine to children of this age.
"Not only will it help protect them from flu, it will help stop the virus spreading to others."
For more information see www.immunisationscotland.org.uk/childflu or call the NHS on 0800 22 44 88.