Close to 50 per cent of young children in Lincolnshire were not vaccinated when flu season hit, according to Public Health England.
The latest figures show that just 51 per cent of four to ten-year-olds had received the flu vaccine at the end of November.
That's slightly higher than the rate across England, where 47 per cent of primary school children were up to date on their annual dose.
Of 50,086 primary school children in Lincolnshire, 24,504 had not been given the vaccine, which is delivered in school as a nasal spray.
Public Health England advises headteachers to make sure their pupils are protected before the winter months.
Of the youngest children eligible, in reception, 54 per cent had been given the spray - slightly more than the 46 per cent among the oldest, in year five.
The flu vaccine programme runs from the beginning of September to the end of January, with Public Health England (PHE) reporting uptake rates throughout the winter.
The NHS says it's important to make sure children are vaccinated as early as possible.
Dr Richard Pebody, head of flu at PHE, said: "Flu can be nasty for little children. Some develop a very high fever or complications of flu, such as bronchitis or pneumonia, and may need hospital treatment.
"Children also tend to be super-spreaders of flu, so if they get it, they are likely to infect more vulnerable older family members.
"The best form of protection against flu is to get the vaccine if you are eligible, and to practise good respiratory and hand hygiene."
Dr David Elliman, immunisation expert at the Royal College of Paediatrics and Child Health, said that uptake of the flu vaccine is always lower than other routine jabs.
He added: "But even with a modest uptake you see a reduction of flu in the general community. Any uptake is better than nothing."
Last winter was the worst flu season in a decade in England, causing 3,175 hospital admissions and 320 deaths.