The contractor will build Countess Gytha School on higher ground in Queen Camel next to a medical centre.
The existing building next to the River Cam sustained significant damage in 2008.
Features will include six classrooms, an administration area, a sports and dining hall along with a kitchen.
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A multi-use games area and sports field will also be built outside the school.
To help with flood prevention, an attenuation pond will be developed to take all service water from the building.
Craig Allen, Construction Director, said: "BAM is delighted to play its part in providing more modern facilities for pupils – which most importantly will be at far lower risk of flooding.
"We will work hard as always to ensure we do our best for the local environment and community while producing a first class building for pupils and staff at the school."
Work began on site in June 2015 and is scheduled for completion in 2016.
(LM/CD)
