HolyCross Girls Primary School, at the centre of a bitter three-month picket by Protestant residents in north Belfast last year, has seen applications drop by over one third.
The school's principal, Ms Anne Tanney, said while she was disappointed that only 19 pupils instead of the normal average of 30 had applied for primary one at the Catholic school for the next academic year, she fully understood parents' anxieties about sending their daughters to the Ardoyne-based school.
"The terrible situation we have had has certainly affected numbers," she told The Irish Times.
"Many of the parents who are still undecided about sending their girls to us have told me that this is nothing personal against the school. They are simply worried, not knowing how the situation is going to develop. If things stay quiet, though, I hope that we will be making a full recovery next year."
For 12 weeks last autumn, the girls and their parents had to run a daily gauntlet of verbal and physical abuse from residents of the loyalist Glenbryn estate who were protesting against alleged republican attacks on their homes.
A security operation costing millions of pounds was in place for months to guarantee pupils and parents' safety on the way to and from school. The protest was eventually called off in December after a package of measures for the area was agreed by politicians and community representatives but sectarian clashes flared up again close to the school in January.
Ms Tanney said she was pleased with her pupils' Eleven Plus transfer test results, which determine whether children attend grammar or secondary schools after their primary education. "We would regard all the girls as a success. Even just for them to have been able to do the exam under the circumstances is a huge achievement," she added.
Almost half of the school's 200 children were still receiving counselling, said Ms Tanney.