Bellarena PS, situated on the Sea Coast Road near Limavady – is to close in August – four years after a nearby Catholic primary also shut.
Department of Education Permanent Secretary Derek Baker said there were clear sustainability issues.
It experienced declining enrolment and had only 24 pupils last year.
Mr Baker said numbers had been on a downward trajectory over time, and the school now had two composite classes spanning four and three year groups.
“Notwithstanding a healthy accumulated surplus position, the school does not currently operate within its in-year budget,” Mr Baker said.
“The overall demographic projections for the local government district anticipate further slight decreases in the 0-15 years cohort over the next five years.
“There are four alternative Controlled primary schools, and other primary schools of a different management type, within a 10 mile radius, all with available places and assessed by the Education and Training Inspectorate as good or better.”
The Education Authority said closing the school would give children better opportunities “to engage in education and in after school activities through larger classes and mixing with their peers”.
Opponents said the plan failed to take account of positive aspects of small schools including “exceptional staff commitment, close parental contact, and a nurturing family atmosphere”.
Parents also asked that the school be considered for transformation to integrated status “as it is already integrated but in name”.
The neighbouring St Anthony’s Primary School closed in 2015.