Department for Education data shows 87.5 percent of pupils starting secondary school in Lincolnshire in September have been offered a place at their preferred school – down from 90.3 percent last year.
It means 983 children have missed out on their top choice.
Martin Smith, assistant director for education at LIncolnshire County Council, said: "One of the council's priorities is that all local children get a good education, and we are pleased that the overwhelming majority of children get a place at their first-choice school.
"We realise it's upsetting for those who don't, but we are confident that they will still have a positive experience at a secondary school in their area.
"We want all schools to be at least good, and we support wherever we can assist, although responsibility for the quality of provision at academies lies with the Regional Schools Commissioner, who we work closely with."
The figures also show the number of applications to secondary schools in Lincolnshire has remained in line with last year's 7,857.
Meanwhile, the proportion of primary school pupils who have been offered their first choice of school is up slightly from 94 percent last year to 95.5 percent.
Across England, the proportion of children receiving an offer from their preferred primary school rose to 91.8 percent, from 90.2 percent last year.
Geoff Barton, general secretary of the Association of School and College Leaders, said: “Most pupils gain places at their first-choice schools, but a significant number, particularly at secondary level, don’t do so, and this is bound to be very disappointing for the families concerned.
“The solution is for the Government to put more support into struggling schools and make sure every family has access to a good school place.
“Unfortunately, the current system is not working well enough for schools which face the greatest degree of challenge and the communities they serve.”
School standards minister Nick Gibb said: “For the fourth consecutive year more than 90% of children have been offered a place at either their top primary school choice or one of their top three secondary school choices, which I know means a huge amount to families.
“Children and young people are now vastly more likely to be at a good or outstanding school than they were 10 years ago, so parents across the country can be confident their child will get the high-quality education they deserve.”
The DfE said several local authorities had advised that a larger than usual number of applications were submitted late. Those are not included in these figures.
The DfE added that there might be an increase in the number of families opting to home school due to the pandemic, while a reduction in migration, because of the pandemic travel controls, may have contributed to the fall.