North Ronaldsay Primary School's single classroom will be kept on standby from August as Teigan Scott, 12, moves to secondary in Kirkwall.
Orkney's most northerly island only has a population of about 50 people.
Orkney Islands Council said the school would be brought back into use if more families with young children moved to the island.
The building is also used by community groups.
Island residents have blamed poor transport links for the lack of young families.
Teigan told the BBC she was looking forward to moving on to secondary but worried for the future of her former school.
"I am excited to go up to the bigger school," she said.
"But I have a tiny little drop of sadness because the school will be closing and the island might fall apart."