Springwell Harrogate on Grove Road - previously The Grove Academy - caters for pupils with social, emotional and mental health needs.
It joined the Wellspring Academy Trust just weeks after schools were ordered to shut in March having previously been run by Delta Academies Trust and North Yorkshire County Council.
During the lockdown period, Wellspring said it has "substantially" upgraded the school’s facilities, including renovating the entire ground floor to create four classrooms and a new food technology area.
Mark Wilson, chief executive of the trust, said: “We are thrilled to be able to welcome Springwell Harrogate to our trust. It plays an essential role in supporting young people and their families in the Harrogate area and we are proud to have been chosen to ensure that that support continues and develops.
“The investment we have made in the school will improve the day to day experience for the pupils and demonstrates our commitment to the Harrogate community."
The move comes after county council bosses facing spiralling high needs education costs last year introduced a new model for alternative provision and specialist schools in North Yorkshire.
It saw funding shifted from its pupil referral service to new school partnerships with mainstream schools.
At the time, union officials representing Grove Academy staff said that the "severity of the council’s cuts" meant that staff and resources could not be maintained and redundancies were expected.
The county council previously said Wellspring has "a track record in special school and alternative provision" as it approved the take over under new funding arrangements in 2019.
Wellspring is a large multi-academy trust currently which runs 25 primary, secondary, special schools across the Yorkshire and Greater Lincolnshire region.
The trust has built eight new schools around the region and operates a number of non-profit and charitable enterprises.
Mr Wilson added: "The Springwell Harrogate and wider Wellspring team has enjoyed welcoming pupils back after the extended break and getting them settled into their new look school.”
By Jacob Webster, Local Democracy Reporter