Balfour Beatty and BAM are competing to build the £11.7m Kearsley Academy.
The two companies will now work up detailed bids for consideration by council representatives and academy sponsors in August.
The lead sponsor for the academy is Northern Education. The co-sponsor is Bolton Council, with the University of Bolton as the education partner.
The academy, formerly known as George Tomlinson School, will accommodate 950 pupils, from 11- to 18-years-old.
As with the Essa and St Catherine's, the new academy will remain part of the Bolton family of schools.
Once the preferred bidder is chosen, the school will benefit from a complete rebuild, including a new sixth form college, with work potentially beginning early next year.