All of St George's School will move to the Wanganui Collegiate School campus next year, losing its Year 1-3 pupils in the process.
Whanganui College Board deputy chair David Cole said there were "very few" children in those junior years.
Whanganui College Board runs both St George's and Wanganui Collegiate.
The move is a reaction to the low roll at St George's - numbers have dropped to 147, from a high of more than 300 in the 1980s. St George's applied to become an integrated school with state funding, but that was declined earlier this year.
The fate of its Grey St buildings and grounds has yet to be determined. Mr Cole said there were no definite plans as yet.
Staffing for the shifted school is also still being discussed by the board. From next year, St George's Year 5 to 8 pupils will be permanently based at Wanganui Collegiate. Children in Year 3 this year will be accommodated next year in a Year 4 and 5 composite class.
The school's Year 7 and 8 pupils are already at Collegiate. They were moved there at the beginning of this year.
Whanganui College Board of Trustees chairwoman Tam Jex-Blake said they had benefited enormously from specialist teaching at Collegiate, and from resources like the technology block and the Izard Sports Centre. At Collegiate, St George's pupils are to be based mainly in Empson House. The board is committed to adding a separate and stand-alone building for them when possible.
The departure of the junior students, and loss of the Grey St premises, saddened St George's parents' working group spokesman Jamie Doble. "I do believe that it is important to retain independent education of high quality in Wanganui, and so the Parents and Friends Association and the parent working group will work with the school staff and the board to ensure that the school we all love can prosper in the future," he said.
The shift to Collegiate and dropping of junior classes was a bold move, but would ensure the school's survival, Mrs Jex-Blake said. "The cost-effectiveness of this arrangement compared to that of maintaining a similar level of offering at Grey St provides a sound business model that will ensure St George's flourishes well into the future," she said.
ST GEORGE'S
1927 - began as boarding school for boys aged 8 to 13
1980 - became a day school and included girls
1980s - roll grew to more than 300 and pupils accepted from age 5
2005 - roll began to decline
2011 - roll at 147, state funding declined, Years 7-8 moved to Collegiate
2012 - Years 4-8 to move to Collegiate, Years 1-3 dropped