Bedford Free School has been granted planning permission on appeal.
Planning bosses at Borough Hall have had their earlier decision by the government, and the school which opened in September has been given the go-ahead to continue at its town centre site.
Ian Pryce, the chair of governors at the school who is also CEO of Bedford College which project-managed the school, said that it was now time to move on.
He said: “This has been a lengthy and difficult process for everyone. We all want the same thing – better educated young people, we just differ on how to achieve that.
“Our research showed this was a school the community wanted and our first year intake reflected that. There were legitimate questions to be asked about the effect of the school on local traffic but changes in college activity meant there are now fewer people moving across Cauldwell Street.
“Our advice has been clear throughout that planning consent would be achieved. While we accept the Borough’s planning decision stemmed from genuine concern by members, it is a shame that it lengthened the process, and unsettled parents and pupils at an important time.
“I am sure everyone will now move on and our job is to establish the Free School as an important part of the Bedford family of schools.”
Bedford Free School opened at the beginning of the current school year, and is a secondary school for students aged 11-16.
The school is based in Cauldwell House in Cauldwell Street, and planning permission was previously refused because of concerns about traffic.
Nigel Syson, the chair designate of the school, said: “We are delighted with the appeal result and we take this opportunity to thank our parents for the support and loyalty they have shown throughout.
“They have been determined to ensure their children access the opportunity of an excellent state school education.
“We hope now that Mark Lehain and his team will be able to concentrate on what matters most: the education of our pupils.”
A spokesman for Bedford Borough Council said: “The Free School has been granted by planning permission by the Secretary of State. This overrules the decision taken locally.”