Carol White, director of children and young people's services for Calderdale Council, said yesterday there would be a new build, after the council was criticised at Thursday night's public meeting.
She said: "I can confirm the academy will be a new build."
The Holmfield secondary is due to be replaced with an academy in 2010.
Information about the closure and the plans for the new school was given out to about 150 people at three informal consultation meetings held by Calderdale Council.
The academy will open in Holy Trinity's buildings, and transfer to new facilities in 2012.
The exact nature of the proposed new buildings has not yet been agreed.
Calderdale Council, one of the co-sponsors, along with Huddersfield University and Calder-dale College, will be responsible for getting the academy built once a design has been agreed.
Jim Miller, acting NUT divisional secretary had previously accused the council of making do with a refubishment of the academy.
He said: "It is clearly a done deal as the council clearly stated 'when' Holy Trinity closes, not 'if'."
Ms White said: "Any final decision by the council to approve closure of Holy Trinity will not be taken until February 2009 once the consultation on the academy is finished."
There will be 1,500 students in the academy. More public meetings will be held in November.