Closing Castle Caereinion could save the council £58,100 a year.
However paying transport costs for just 16 pupils to the nearest Church in Wales school in Welshpool would set back the council £32,700.
Members of Powys County Council's cabinet meeting on Tuesday, voted unanimously to close Castle Caereinion Church in Wales primary school.
Meanwhile Llanfair Caereinion primary school and Caereinion High School will merge over the summer and when the all through school opens its doors in September 2022 – it will be known as Ysgol Bro Caereinion.
Adult social care and Welsh language portfolio holder Councillor Myfanwy Alexander urged parents to send their children to the merged schools.
The former head girl at Caereinion High School, said: “Many of the children currently attending Castle Caereinion will be within the catchment of a new all age school in Llanfair Caereinion.
“We know that the new curriculum will be able to be delivered more easily in all age schools and that why it’s part of our education transformation policy.
“With the best will in the world a small rural school can’t provide access to science labs or recreational facilities for sport.
“Those who move west from Castle Caereinion will be going to a bilingual school which will allow them to have access to Welsh provision that’s not currently available to them.
“Part of the provision of the new school is to allow enhanced Welsh learning for children in every stream, so there are new opportunities available for those young people.”
In past meetings, assurances had been given that parents who wish their children to continue attending a church school would be given free transport with Welshpool Church in Wales primary school the nearest.
School transformation manager, Marianne Evans said: “We will be providing transport to Welshpool Church in Wales school for any pupil who wishes to.
“It will be done on a case-by-case basis and will be available to pupils currently at Castle Caereinion.
In total 21 objections were received against the closure including one from the St Asaph diocese and Castle Caereinion community council. A petition against the closure was signed by 102 people.