Fife Council has written to Crombie Primary School parents telling them the Scottish Government has given the go-ahead for its closure.
Crombie was proposed for closure as part of a Fife Council review of the region school estate.
It claims its programme will improve the condition and suitability of its schools and the overall learning environment and experience for children.
The programme also aims to reduce the number of spare classroom places across Fife.
Councillor Bryan Poole, Fife Council’s executive spokesman for education, children, young people and families, said: “Closing a school is not something that is done without long and careful consideration.
“As a council we have a duty to provide the best service and the best value for money for all of the children and families in Fife. We simply can’t continue to provide that level of service if huge amounts of our budgets are taken up maintaining deteriorating school buildings.
“We should be spending that money in more meaningful ways, providing the very best learning environment which will help our teachers to continue to improve the learning experiences of our young people. This decision will help us do just that.”
Catchment areas will now be rezoned and children from Crombie Primary School will move to Limekilns Primary School.
Fife Council education service has pledged to working closely with parents, children and staff to help them through the process.
Mr Poole added: “I understand that closing any school creates concerns for parents, but as councillors for the whole of Fife we have a responsibility to consider what is in the longer term, best interests of all children in Fife.
“It was on that basis that we considered the school rationalisation programme. I’d like to thank the parents, staff and the local community for the dignity and patience they have shown throughout this process.
“As plans are put in place to support the transfer of pupils to their new school I hope they will continue to work with us as we move on with the process.”
Dunfermline Labour MSP Cara Hilton said: “I supported the community’s wish for the decision to be called in and it’s disappointing the SNP minister has decided not to take this opportunity.
“I pay tribute to all involved in this local campaign, and particularly the determination of (campaigner) Tony Orton. This decision will come as a real blow to Crombie.
“It is now in the best interests of the parents and children involved that a smooth transition process to their new school in Limekilns is put in place, and I will be seeking assurances from Fife Council that this will happen”.