The decision by Shetland Islands Council to close the Skerries secondary will not be called in by Scottish ministers.
That means the department will close on 4th July, after which pupils will receive their lessons at the Anderson High School in Lerwick.
A transition group will be established within the council to help assist with the move.
The SIC says the group will plan the transition of pupils, and ensure youngsters are supported in getting used to their new learning environment at the Anderson High and the hostel.
Meanwhile, ferry officials will be asked to alter the timetable to allow pupils to commute to Lerwick on Mondays instead of Sunday evenings.
Chairwoman of education and families, Vaila Wishart said: “This has been a long and difficult process, and parents and pupils at Skerries school secondary department will undoubtedly be disappointed with the ministers’ decision.
“However, we can reassure them that our main aim now is to make the transfer as seamless as possible, and to support pupils throughout the coming months.
“I will be asking officials to look into the possibility of changing the ferry times so the pupils can come out on Monday mornings instead of Sunday nights as commented on by the Scottish ministers.”